Gonococcal proteins and nucleic acids

ABSTRACT

The invention provides proteins from gonococcus ( Neisseria gonorrhoeae ), including amino acid sequences, the corresponding nucleotide sequences, expression data, and serological data. The proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. They are also useful for distinguishing between gonococcus and meningococcus and, in particular, between gonococcus and serogroup B meningococcus.

TECHNICAL FIELD

This invention relates to proteins from the bacterium Neisseria gonorrhoeae, and more particularly to such proteins which do not have corresponding homologs or orthologs in serogroup B N.meningitidis.

BACKGROUND ART

Neisseria gonorrhoeae is a bacterial pathogen. There is currently no effective vaccine against N.gonorrhoeae infection. It is an object of the invention to provide proteins and nucleic acid useful in vaccine study and/or manufacture.

N.gonorrhoeae is related to N.meningitidis. Sequence data are now available for serogroup B of meningococcus [e.g. WO99/24578; WO99/36544; WO99/57280; WO00/22430; WO00/66791; Tettelin et al. (2000) Science 287:1809-1815] and also for serogroup A [Parkhill et al. (2000) Nature 404:502-506]. It is a further object of the invention to provide proteins and nucleic acid useful in distinguishing between gonococcus and meningococcus and, in particular, between gonococcus and serogroup B meningococcus.

DISCLOSURE OF THE INVENTION

The invention provides proteins comprising the N.gonorrhoeae amino acid sequences disclosed in the examples (the even-numbered SEQ IDS 2 to 8622). 159 of these have no homolog in serogroup B meningococcus and these have been given a name in the form “NGSn”.

It also provides proteins comprising amino acid sequences having sequence identity to the N.gonorrhoeae amino acid sequences disclosed in the examples. Depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g. 60%, 70%, 80%, 90%, 95%, 99% or more). These proteins include homologs, orthologs, allelic variants and functional mutants. Typically, 50% identity or more between two proteins is considered to be an indication of functional equivalence. Identity between proteins is preferably determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty=12 and gap extension penalty=1.

The invention further provides proteins comprising fragmnents of the N.gonorrhoeae amino acid sequences disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the sequences and, depending on the particular sequence, n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more). Preferably the fragments comprise one or more epitopes from the sequence. Other preferred fragments are (a) the N-terminal signal peptides of the proteins disclosed in the examples, and (b) the proteins disclosed in the examples, but without their N-terminal signal peptides.

The proteins of the invention can, of course, be prepared by various means (e.g. recombinant expression, purification from Neisseria, chemical synthesis etc.) and in various forms (e.g. native, fusions etc.). They are preferably prepared in substantially pure form (i.e. substantially free from other N.gonorrhoeae or host cell proteins).

The proteins of the invention are preferably Neisserial proteins, more preferably N.gonorrhoeae proteins.

The invention provides antibodies which bind to these proteins. These may be polyclonal or monoclonal and may be produced by any suitable means. The antibodies may include a detectable label.

The invention provides nucleic acid comprising the N.gonorrhoeae nucleotide sequences disclosed in the examples. In addition, the invention provides nucleic acid comprising nucleotide sequences having sequence identity to the N.gonorrhoeae nucleotide sequences disclosed in the examples.

Furthermore, the invention provides nucleic acid which can hybridise to the N.gonorrhoeae nucleic acid disclosed in the examples, preferably under “high stringency” conditions (e.g. 65° C. in a 0.1×SSC, 0.5% SDS solution).

Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least n consecutive nucleotides from the N.gonorrhoeae sequences and, depending on the particular sequence, n is 10 or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200 or more).

The invention also provides nucleic acid encoding the proteins and protein fragments of the invention.

The invention includes nucleic acid comprising sequences complementary to those described above (e.g. for antisense or probing purposes).

Nucleic acid according to the invention can be prepared in many ways (e.g. by chemical synthesis, from genomic or cDNA libraries, from the organism itself etc.) and can take various forms (e.g. single stranded, double stranded, vectors, probes etc.).

In addition, the term “nucleic acid” includes DNA and RNA, and also their analogues, such as those containing modified backbones, and also peptide nucleic acids (PNA) etc.

The invention provides vectors comprising nucleotide sequences of the invention (e.g. cloning or expression vectors) and host cells transformed with such vectors.

The invention provides compositions comprising protein, antibody, and/or nucleic acid according to the invention. These compositions may be suitable as immunogenic compositions, for instance, or as diagnostic reagents, or as vaccines.

The invention also provides nucleic acid, protein, or antibody according to the invention for use as medicaments (e.g. as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid, protein, or antibody according to the invention in the manufacture of: (i) a medicament for treating or preventing infection due to Neisseria; (ii) a diagnostic reagent for detecting the presence of Neisseria or of antibodies raised against Neisseria; and/or (iii) a reagent which can raise antibodies against Neisseria. Said Neisseria may be any species, but is preferably N.gonorrhoeae.

The invention also provides a method of treating a patient, comprising administering to the patient a therapeutically effective amount of nucleic acid, protein, and/or antibody of the invention.

According to further aspects, the invention provides various processes.

A process for producing proteins of the invention is provided, comprising the step of culturing a host cell of to the invention under conditions which induce protein expression.

A process for producing protein or nucleic acid of the invention is provided, wherein the protein or nucleic acid is synthesised in part or in whole using chemical means.

A process for detecting polynucleotides of the invention is provided, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridising conditions to form duplexes; and (b) detecting said duplexes.

A process for detecting proteins of the invention is provided, comprising the steps of: (a) contacting an antibody of the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.

A process for distinguishing N.gonorrhoeae from N.meningitidis is provided, comprising the steps of: (a) contacting an antibody of the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes. Alternatively, the steps may be (a) contacting nucleic acid of the invention with a biological sample under conditions suitable for the nucleic acid hybridisation; and (b) detecting any such hybridisation. Alternatively, the steps may be (a) contacting a protein of the invention with a biological sample (e.g. blood or serum) under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.

A summary of standard techniques and procedures which may be employed in order to perform the invention (e.g. to utilise the disclosed sequences for vaccination or diagnostic purposes) follows. This summary is not a limitation on the invention, but gives examples that may be used, but are not required.

General

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature eg. Sambrook Molecular Cloning; A Laboratory Manual, Second Edition (1989) or Third Edition (2000); DNA Cloning, Volumes I and II (D. N Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription and Translation (B. D. Hames & S. J. Higgins eds. 1984); Animal Cell Culture (R. I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); the Methods in Enzymology series (Academic Press, Inc.), especially volumes 154 & 155; Gene Transfer Vectors for Mammalian Cells (J. H. Miller and M. P. Calos eds. 1987, Cold Spring Harbor Laboratory); Mayer and Walker, eds. (1987), Immunochemical Methods in Cell and Molecular Biology (Academic Press, London); Scopes, (1987) Protein Purification: Principles and Practice, Second Edition (Springer-Verlag, N.Y.), and Handbook of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell eds 1986).

Standard abbreviations for nucleotides and amino acids are used in this specification.

Definitions

A composition containing X is “substantially free of” Y when at least 85% by weight of the total X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95% or even 99% by weight.

The term “comprising” means “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.

The term “heterologous” refers to two biological components that are not found together in nature; The components may be host cells, genes, or regulatory regions, such as promoters. Although the heterologous components are not found together in nature, they can function together, as when a promoter heterologous to a gene is operably linked to the gene. Another example is where a Neisseria sequence is heterologous to a mouse host cell. A further examples would be two epitopes from the same or different proteins which have been assembled in a single protein in an arrangement not found in nature.

An “origin of replication” is a polynucleotide sequence that initiates and regulates replication of polynucleotides, such as an expression vector. The origin of replication behaves as an autonomous unit of polynucleotide replication within a cell, capable of replication under its own control. An origin of replication may be needed for a vector to replicate in a particular host cell. With certain origins of replication, an expression vector can be reproduced at a high copy number in the presence of the appropriate proteins within the cell, Examples of origins are the autonomously replicating sequences, which are effective in yeast; and the viral T-antigen, effective in COS-7 cells.

A “mutant” sequence is defined as DNA, RNA or amino acid sequence differing from but having sequence identity with the native or disclosed sequence. Depending on the particular sequence, the degree of sequence identity between the native or disclosed sequence and the mutant sequence is preferably greater than 50% (eg. 60%, 70%, 80%, 90%, 95%, 99% or more, calculated using the Smith-Waterman algorithm as described above). As used herein, an “allelic variant” of a nucleic acid molecule, or region, for which nucleic acid sequence is provided herein is a nucleic acid molecule, or region, that occurs essentially at the same locus in the genome of another or second isolate, and that, due to natural variation caused by, for example, mutation or recombination, has a similar but not identical nucleic acid sequence. A coding region allelic variant typically encodes a protein having similar activity to that of the protein encoded by the gene to which it is being compared. An allelic variant can also comprise an alteration in the 5′ or 3′ untranslated regions of the gene, such as in regulatory control regions (eg. see U.S. Pat. No. 5,753,235).

Expression Systems

The Neisseria nucleotide sequences can be expressed in a variety of different expression systems; for example those used with mammalian cells, baculoviruses, plants, bacteria, and yeast.

i. Mammalian Systems

Mammalian expression systems are known in the art. A mammalian promoter is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5′ end of the coding sequence, and a TATA box, usually located 25-30 base pairs (bp) upstream of the transcription initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element, usually located within 100 to 200 bp upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation [Sambrook et al. (1989) “Expression of Cloned Genes in Mammalian Cells.” In Molecular Cloning: A Laboratory Manual, 2nd ed.].

Mammalian viral genes are often highly expressed and have a broad host range; therefore sequences encoding mammalian viral genes provide particularly useful promoter sequences. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter (Ad MLP), and herpes simplex virus promoter. In addition, sequences derived from non-viral genes, such as the murine metallotheionein gene, also provide useful promoter sequences. Expression may be either constitutive or regulated (inducible), depending on the promoter can be induced with glucocorticoid in hormone-responsive cells.

The presence of an enhancer element (enhancer), combined with the promoter elements described above, will usually increase expression levels. An enhancer is a regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to homologous or beterologous promoters, with synthesis beginning at the normal RNA start site. Enhancers are also active when they are placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation, or at a distance of more than 1000 nucleotides from the promoter [Maniatis et al. (1987) Science 236:1237; Alberts et al. (1989) Molecular Biology of the Cell, 2nd ed.]. Enhancer elements derived from viruses may be particularly useful, because they usually have a broader host range. Examples include the SV40 early gene enhancer [Dijkema et al (1985) EMBO J. 4:7611 and the enhancer/promoters derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus [Gorman et al. (1982b) Proc. Natl. Acad. Sci. 79:6777] and from human cytomegalovirus [Boshart et al. (1985) Cell 41:521]. Additionally, some enhancers are regulatable and become active only in the presence of an inducer, such as a hormone or metal ion [Sassone-Corsi and Borelli (1986) Trends Genet. 2:215; Maniatis et al. (1987) Science 236:1237].

A DNA molecule may be expressed intracellularly in mammalian cells. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in mammalian cel Whitelaw (1988) “Termination and 3′ end processing of eukaryotic RNA, In Transcription and splicing (ed. B. D. Hames and D. M. Glover); Proudfoot (1989) Trends Biochem. Sci. 14:105]. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminater/polyadenylation signals include those derived from SV40 [Sambrook et al (1989) “Expression of cloned genes in cultured mammalian cells.” In Molecular Cloning: A Laboratory Manual].

Usually, the above described components, comprising a promoter, polyadenylation signal, and transcription termination sequence are put together into expression constructs. Enhancers, introns with functional splice donor and acceptor sites, and leader sequences may also be included in an expression construct, if desired. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as mammalian cells or bacteria. Mammalian replication systems include those derived from animal viruses, which require trans-acting factors to replicate. For example, plasmids containing the replication systems of papovaviruses, such as SV40 [Gluzman (1981) Cell 23:175] or polyomavirus, replicate to extremely high copy number in the presence of the appropriate viral T antigen. Additional examples of mammalian replicons include those derived from bovine papillomavirus and Epstein-Barr virus. Additionally, the replicon may have two replicaton systems, thus allowing it to be maintained, for example, in mammalian cells for expression and in a prokaryotic host for cloning and amplification. Examples of such mammalian-bacteria shuttle vectors include pMT2 [Kaufman et al. (1989) Mol. Cell. Biol. 9:946] and pHEBO [Shimizu et al. (1986) Mol. Cell. Biol. 6:1074].

The transformation procedure used depends upon the host to be transformed. Methods for introduction of heterologous polynucleotides into mammalian cells are known in the art and include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including but not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular carcinoma cells (eg. Hep G2), and a number of other cell lines.

ii. Baculovirus Systems

The polynucleotide encoding the protein can also be inserted into a suitable insect expression vector, and is operably linked to the control elements within that vector. Vector construction employs techniques which are known in the art. Generally, the components of the expression system include a transfer vector, usually a bacterial plasmid, which contains both a fragment of the baculovirus genome, and a convenient restriction site for insertion of the heterologous gene or genes to be expressed; a wild type baculovirus with a sequence homologous to the baculovirus-specific fragment in the transfer vector (this allows for the homologous recombination of the heterologous gene in to the baculovirus genome); and appropriate insect host cells and growth media.

After inserting the DNA sequence encoding the protein into the transfer vector, the vector and the wild type viral genome are transfected into an insect host cell where the vector and viral genome are allowed to recombine. The packaged recombinant virus is expressed and recombinant plaques are identified and purified. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego Calif. (“MaxBac” kit). These techniques are generally known to those skilled in the art and fully described in Summers & Smith, Texas Agricultural Experiment Station Bulletin No.1555(1987) (“Summers & Smith”).

Prior to inserting the DNA sequence encoding the protein into the baculovirus genome, the above described components, comprising a promoter, leader (if desired), coding sequence, and transcription termination sequence, are usually assembled into an intermediate transplacement construct (transfer vector). This may contain a single gene and operably linked regulatory elements; multiple genes, each with its owned set of operably linked regulatory elements; or multiple genes, regulated by the same set of regulatory elements. Intermediate transplacement constructs are often maintained in a replicon, such as an extra-chromosomal element (e.g. plasmids) capable of stable maintenance in a host, such as a bacterium. The replicon will have a replication system, thus allowing it to be maintained in a suitable host for cloning and amplification.

Currently, the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373. Many other vectors, known to those of skill in the art, have also been designed. These include, for example, pVL985 (which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamH1 cloning site 32 basepairs downstream from the ATT; see Luckow and Summers, Virology (1989)17:31.

The plasmid usually also contains the polyhedrin polyadenylation signal (Miller et al. (1988) Ann. Rev. Microbiol., 42:177) and a prokaryotic ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. coli.

Baculovirus transfer vectors usually contain a baculovirus promoter. A baculovirus promoter is any DNA sequence capable of binding a baculovirus RNA polymerase and initiating the downstream (5′to 3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A baculovirus transfer vector may also have a second domain called an enhancer, which, if present, is usually distal to the structural gene. Expression may be either regulated or constitutive.

Structural genes, abundantly transcribed at late times in a viral infection cycle, provide particularly useful promoter sequences. Examples include sequences derived from the gene encoding the viral polyhedron protein, Friesen et al., (1986) “The Regulation of Baculovirus Gene Expression,” in: The Molecular Biology of Baculoviruses (ed. Walter Doerfler); EPO Publ. Nos. 127 839 and 155 476; and the gene encoding the p10 protein, Vlak et al., (1988), J. Gen. Virol. 69:765.

DNA encoding suitable signal sequences can be derived from genes for secreted insect or baculovirus proteins, such as the baculovirus polyhedrin gene (Carbonell et al. (1988) Gene, 73:409). Alternatively, since the signals for mammalian cell posttranslational modifications (such as signal peptide cleavage, proteolytic cleavage, and phosphorylation) appear to be recognized by insect cells, and the signals required for secretion and nuclear accumulation also appear to be conserved between the invertebrate cells and vertebrate cells, leaders of non-insect origin, such as those derived from genes encoding human α-interferon, Maeda et al., (1985), Nature 315:592; human gastrin-releasing peptide, Lebacq-Verheyden et al., (1988), Molec. Cell. Biol. 8:3129; human IL-2, Smith et al., (1985) Proc. Nat'l Acad. Sci. USA, 82:8404; mouse IL-3, (Miyajima et al., (1987) Gene 58:273; and human glucocerebrosidase, Martin et al. (1988) DNA, 7:99, can also be used to provide for secretion in insects.

A recombinant polypeptide or polyprotein may be expressed intracellularly or, if it is expressed with the proper regulatory sequences, it can be secreted. Good intracellular expression of nonfused foreign proteins usually requires heterologous genes that ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. If desired, methionine at the N-terminus may be cleaved from the mature protein by in vitro incubation with cyanogen bromide.

Alternatively, recombinant polyproteins or proteins which are not naturally secreted can be secreted from the insect cell by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provides for secretion of the foreign protein in insects. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the translocation of the protein into the endoplasmic reticulum.

After insertion of the DNA sequence and/or the gene encoding the expression product precursor of the protein, an insect cell host is co-transformed with the heterologous DNA of the transfer vector and the genomic DNA of wild type baculovirus—usually by co-transfection. The promoter and transcription termination sequence of the construct will usually comprise a 2-5 kb section of the baculovirus genome. Methods for introducing heterologous DNA into the desired site in the baculovirus virus are known in the art. (See Summers & Smith supra; Ju et al. (1987); Smith et al., Mol. Cell. Biol. (1983) 3:2156; and Luckow and Summers (1989)). For example, the insertion can be into a gene such as the polyhedrin gene, by homologous double crossover recombination; insertion can also be into a restriction enzyme site engineered into the desired baculovirus gene. Miller et al., (1989), Bioessays 4:91.The DNA sequence, when cloned in place of the polyhedrin gene in the expression vector, is flanked both 5′ and 3′ by polyhedrin-specific sequences and is positioned downstream of the polyhedrin promoter.

The newly formed baculovirus expression vector is subsequently packaged into an infectious recombinant baculovirus. Homologous recombination occurs at low frequency (between about 1% and about 5%); thus, the majority of the virus produced after cotransfection is still wild-type virus. Therefore, a method is necessary to identify recombinant viruses. An advantage of the expression system is a visual screen allowing recombinant viruses to be distinguished. The polyhedrin protein, which is produced by the native virus, is produced at very high levels in the nuclei of infected cells at late times after viral infection. Accumulated polyhedrin protein forms occlusion bodies that also contain embedded particles. These occlusion bodies, up to 15 μm in size, are highly refractile, giving them a bright shiny appearance that is readily visualized under the light microscope. Cells infected with recombinant viruses lack occlusion bodies. To distinguish recombinant virus from wild-type virus, the transfection supernatant is plaqued onto a monolayer of insect cells by techniques known to those skilled in the art. Namely, the plaques are screened under the light microscope for the presence (indicative of wild-type virus) or absence (indicative of recombinant virus) of occlusion bodies. “Current Protocols in Microbiology” Vol. 2 (Ausubel et al. eds) at 16.8 (Supp. 10, 1990); Summers & Smith, supra; Miller et al. (1989).

Recombinant baculovirus expression vectors have been developed for infection into several insect cells. For example, recombinant baculoviruses have been developed for, inter alia: Aedes aegypti , Autographa californica, Bombyx mori, Drosophila melanogaster, Spodoptera frugiperda, and Trichoplusia ni (WO 89/046699; Carbonell et al., (1985) J. Virol. 56:153; Wright (1986) Nature 321:718; Smith et al., (1983) Mol. Cell. Biol. 3:2156; and see generally, Fraser, et al. (1989) In Vitro Cell. Dev. Biol. 25:225).

Cells and cell culture media are commercially available for both direct and fusion expression of heterologous polypeptides in a baculovirus/expression system; cell culture technology is generally known to those skilled in the art. See, eg. Summers & Smith supra.

The modified insect cells may then be grown in an appropriate nutrient medium, which allows for stable maintenance of the plasmid(s) present in the modified insect host. Where the expression product gene is under inducible control, the host may be grown to high density, and expression induced. Alternatively, where expression is constitutive, the product will be continuously expressed into the medium and the nutrient medium must be continuously circulated, while removing the product of interest and augmenting depleted nutrients. The product may be purified by such techniques as chromatography, eg. HPLC, affinity chromatography, ion exchange chromatography, etc.; electrophoresis; density gradient centrifugation; solvent extraction, etc. As appropriate, the product may be further purified, as required, so as to remove substantially any insect proteins which are also present in the medium, so as to provide a product which is at least substantially free of host debris, eg. proteins, lipids and polysaccharides.

In order to obtain protein expression, recombinant host cells derived from the transformants are incubated under conditions which allow expression of the recombinant protein encoding sequence. These conditions will vary, dependent upon the host cell selected. However, the conditions are readily ascertainable to those of ordinary skill in the art, based upon what is known in the art.

iii. Plant Systems

There are many plant cell culture and whole plant genetic expression systems known in the art. Exemplary plant cellular genetic expression systems include those described in patents, such as: U.S. Pat. Nos. 5,693,506; 5,659,122; and 5,608,143. Additional examples of genetic expression in plant cell culture has been described by Zenk, Phytochemistry 30:3861-3863 (1991). Descriptions of plant protein signal peptides may be found in addition to the references described above in Vaulcombe et al., Mol. Gen. Genet. 209:3340 (1987); Chandler et al., Plant Molecular Biology 3:407-418 (1984); Rogers, J. Biol. Chem. 260:3731-3738 (1985); Rothstein et al., Gene 55:353-356 (1987); Whittier et al., Nucleic Acids Research 15:2515-2535 (1987); Wirsel et al., Molecular Microbiology 3:3-14 (1989); Yu et al., Gene 122:247-253 (1992). A description of the regulation of plant gene expression by the phytohormone, gibberellic acid and secreted enzymes induced by gibberellic acid can be found in R. L. Jones and J. MacMillin, Gibberellins: in: Advanced Plant Physiology,. Malcolm B. Wilkins, ed., 1984 Pitman Publishing Limited, London, pp. 21-52. References that describe other metabolically-regulated genes: Sheen, Plant Cell, 2:1027-1038(1990); Maas et al., EMBO J. 9:3447-3452 (1990); Benkel and Hickey, Proc. Natl. Acad. Sci. 84:1337-1339 (1987).

Typically, using techniques known in the art, a desired polynucleotide sequence is inserted into an expression cassette comprising genetic regulatory elements designed for operation in plants. The expression cassette is inserted into a desired expression vector with companion sequences upstream and downstream from the expression cassette suitable for expression in a plant host. The companion sequences will be of plasmid or viral origin and provide necessary characteristics to the vector to permit the vectors to move DNA from an original cloning host, such as bacteria, to the desired plant host. The basic bacterial/plant vector construct will preferably provide a broad host range prokaryote replication origin; a prokaryote selectable marker; and, for Agrobacterium transformations, T DNA sequences for Agrobacterium-mediated transfer to plant chromosomes. Where the heterologous gene is not readily amenable to detection, the construct will preferably also have a selectable marker gene suitable for determining if a plant cell has been transformed. A general review of suitable markers, for example for the members of the grass family, is found in Wilmink and Dons, 1993, Plant Mol. Biol. Reptr, 11(2):165-185.

Sequences suitable for permitting integration of the heterologous sequence into the plant genome are also recommended. These might include transposon sequences and the like for homologous recombination as well as Ti sequences which permit random insertion of a beterologous expression cassette into a plant genome. Suitable prokaryote selectable markers include resistance toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions may also be present in the vector, as is known in the art.

The nucleic acid molecules of the subject invention may be included into an expression cassette for expression of the protein(s) of interest. Usually, there will be only one expression cassette, although two or more are feasible. The recombinant expression cassette will contain in addition to the heterologous protein encoding sequence the following elements, a promoter region, plant 5′ untranslated sequences, initiation codon depending upon whether or not the structural gene comes equipped with one, and a transcription and translation termination sequence. Unique restriction enzyme sites at the 5′ and 3′ ends of the cassette allow for easy insertion into a pre-existing vector.

A heterologous coding sequence may be for any protein relating to the present invention. The sequence encoding the protein of interest will encode a signal peptide which allows processing and translocation of the protein, as appropriate, and will usually lack any sequence which might result in the binding of the desired protein of the invention to a membrane. Since, for the most part, the transcriptional initiation region will be for a gene which is expressed and translocated during germination, by employing the signal peptide which provides for translocation, one may also provide for translocation of the protein of interest. In this way, the protein(s) of interest will be translocated from the cells in which they are expressed and may be efficiently harvested. Typically secretion in seeds are across the aleurone or scutellar epithelium layer into the endosperm of the seed. While it is not required that the protein be secreted from the cells in which the protein is produced, this facilitates the isolation and purification of the recombinant protein.

Since the ultimate expression of the desired gene product will be in a eucaryotic cell it is desirable to determine whether any portion of the cloned gene contains sequences which will be processed out as introns by the host's splicosome machinery. If so, site-directed mutagenesis of the “intron” region may be conducted to prevent losing a portion of the genetic message as a false intron code, Reed and Maniatis, Cell 41:95-105, 1985.

The vector can be microinjected directly into plant cells by use of micropipettes to mechanically transfer the recombinant DNA. Crossway, Mol. Gen. Genet, 202:179-185, 1985. The genetic material may also be transferred into the plant cell by using polyethylene glycol, Krens, et al., Nature, 296, 72-74, 1982. Another method of introduction of nucleic acid segments is high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface, Klein, et al., Nature, 327,70-73, 1987 and Knudsen and Muller, 1991, Planta, 185:330-336 teaching particle bombardment of barley endosperm to create transgenic barley. Yet another method of introduction would be fusion of protoplasts with other entities, either minicells, cells, lysosomes or other fusible lipid-surfaced bodies, Fraley, et al., Proc. Natl. Acad. Sci. USA, 79,1859-1863, 1982.

The vector may also be introduced into the plant cells by electroporation. (Fromm et al., Proc. Natl Acad. Sci. USA 82:5824, 1985). In this technique, plant protoplasts are electroporated in the presence of plasmids containing the gene construct. Electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the plasmids. Electroporated plant protoplasts reform the cell wall, divide, and form plant callus,

All plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be transformed by the present invention so that whole plants are recovered which contain the transferred gene. It is known that practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugarcane, sugar beet, cotton, fruit and other trees, legumes and vegetables. Some suitable plants include, for example, species from the genera Fragaria, Lotus, Medicago, Onobryclis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersion, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Cichorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Hererocallis, Nemesia, Pelargonium, Panicum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucum is, Browaalia, Glycine, Lolium, Zea, Triticum, Sorghum, and Datura.

Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts containing copies of the heterologous gene is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos germinate as natural embryos to form plants. The culture media will generally contain various amino acids and hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as corn and alfalfa. Shoots and roots normally develop simultaneously. Efficient regeneration will depend on the medium, on the genotype, and on the history of the culture. If these three variables are controlled, then regeneration is fully reproducible and repeatable.

In some plant cell culture systems, the desired protein of the invention may be excreted or alternatively, the protein may be extracted from the whole plant. Where the desired protein of the invention is secreted into the medium, it may be collected. Alternatively, the embryos and embryoless-half seeds or other plant tissue may be mechanically disrupted to release any secreted protein between cells and tissues. The mixture may be suspended in a buffer solution to retrieve soluble proteins. Conventional protein isolation and purification methods will be then used to purify the recombinant protein. Parameters of time, temperature pH, oxygen, and volumes will be adjusted through routine methods to optimize expression and recovery of heterologous protein.

iv. Bacterial Systems

Bacterial expression techniques are known in the art. A bacterial promoter is any DNA sequence capable of binding bacterial RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site and a transcription initiation site. A bacterial promoter may also have a second domain called an operator, that may overlap an adjacent RNA polymerase binding site at which RNA synthesis begins. The operator permits negative regulated (inducible) transcription, as a gene repressor protein may bind the operator and thereby inhibit transcription of a specific gene. Constitutive expression may occur in the absence of negative regulatory elements, such as the operator. In addition, positive regulation may be achieved bya gene activator protein binding sequence, which, if present is usually proximal (5′) to the RNA polymerase binding sequence. An example of a gene activator protein is the catabolite activator protein (CAP), which helps initiate transcription of the lac operon in Escherichia coli (E. coli) [Raibaud et al. (1984) Annu. Rev. Genet. 18:173]. Regulated expression may therefore be either positive or negative, thereby either enhancing or reducing transcription.

Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes, such as galactose, lactose (lac) [Chang et al. (1977) Nature 198:1056], and maltose. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp) [Goeddel et al. (1980) Nuc. Acids Res. 8:4057; Yelverton et al. (1981) Nucl. Acids Res. 9:731; U.S. Pat. No. 4,738,921; EP-A-0036776 and EP-A-0121775]. The g-laotamase (bla) promoter system [Weissmann (1981) “The cloning of interferon and other mistakes.” In Interferon 3 (ed. 1. Gresser)], bacteriophage lambda P L [Shimatake et al. (1981) Nature 292:128] and T5 [U.S. Pat. No. 4,689,406] promoter systems also provide useful promoter sequences.

In addition, synthetic promoters which do not occur in nature also function as bacterial promoters. For example, transcription activation sequences of one bacterial or bacteriophage promoter may be joined with the operon sequences of another bacterial or bacteriophage promoter, creating a synthetic hybrid promoter [U.S. Pat. No. 4,551,433]. For example, the tac promoter is a hybrid trp-lac promoter comprised of both trp promoter and lac operon sequences that is regulated by the lac repressor [Amann et al. (1983) Gene 25:167; de Boer et al. (1983) Proc. Natl. Acad. Sci. 80:21]. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. A naturally occurring promoter of non-bacterial origin can also be coupled with a compatible RNA polymerase to produce high levels of expression of some genes in prokaryotes. The bacteriophage T7 RNA polymeraselpromoter system is an example of a coupled promoter system [Studier et al. (1986) J. Mol. Biol. 189:113; Tabor et al. (1985) Proc Natl. Acad. Sci. 82:1074]. In addition, a hybrid promoter can also be comprised of a bacteriophage promoter and an E. coli operator region (EPO-A-0 267 851).

In addition to a functioning promoter sequence, an efficient ribosome binding site is also useful for the expression of foreign genes in prokaryotes. In E. coli, the ribosome binding site is called the Shine-Dalgarno (SD) sequence and includes an initiation codon (ATG) and a sequence 3-9 nucleotides in length located 3-11 nucleotides upstream of the initiation codon [Shine et al. (1975) Nature 254:34]. The SD sequence is thought to promote binding of mRNA to the ribosome by the pairing of bases between the SD sequence and the 3′ and of E. coli 16S rRNA [Steitz et al. (1979) “Genetic signals and nucleotide sequences in messenger RNA.” In Biological Regulation and Development: Gene Expression (ed. R. F. Goldberger)]. To express eukaryotic genes and prokaryotic genes with weak ribosome-binding site [Sambrook et al. (1989) “Expression of cloned genes in Escherichia coli.” In Molecular Cloning: A Laboratory Manual].

A DNA molecule may be expressed intracellularly. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide or by either in vivo on in vitro incubation with a bacterial methionine N-terminal peptidase (EPO-A-O 219 237).

Fusion proteins provide an alternative to direct expression. Usually, a DNA sequence encoding the N-terminal portion of an endogenous bacterial protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the bacteriophage lambda cell gene can be linked at the 5′ terminus of a foreign gene and expressed in bacteria. The resulting fusion protein preferably retains a site for a processing enzyme (factor Xa) to cleave the bacteriophage protein from the foreign gene [Nagai et al. (1984) Nature 309:810]. Fusion proteins can also be made with sequences from the lacZ [Jia et al. (1987) Gene 60:197], trpE [Allen et al. (1987) J. Biotechnol. 5:93; Makoff et al. (1989) J. Gen. Microbiol. 135:11], and Chey [EP-A-0 324 647] genes. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin specific processing-protease) to cleave the ubiquitin from the foreign protein. Through this method, native foreign protein can be isolated [Miller et al. (1989) Bio/Technology 7:698].

Alternatively, foreign proteins can also be secreted from the cell by creating chimeric DNA molecules that encode a fusion protein comprised of a signal peptide sequence fragment that provides for secretion of the foreign protein in bacteria [U.S. Pat. No. 4,336,336]. The signal sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). Preferably there are processing sites, which can be cleaved either in vivo or in vitro encoded between the signal peptide fragment and the foreign gene.

DNA encoding suitable signal sequences can be derived from genes for secreted bacterial proteins, such as the E. coli outer membrane protein gene (ompA) [Masui et al. (1983), in: Experimental Manipulation of Gene Expression; Ghrayeb et al. (1984) EMBO J. 3:2437] and the E. coli alkaline phosphatase signal sequence (phoA) [Oka et al. (1985) Proc. Natl. Acad. Sci. 82:7212]. As an additional example, the signal sequence of the alpha-amylase gene from various Bacillus strains can be used to secrete heterologous proteins from B. subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 244 042].

Usually, transcription termination sequences recognized by bacteria are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Transcription termination sequences frequently include DNA sequences of about 50 nucleotides capable of forming stem loop structures that aid in terminating transcription. Examples include transcription termination sequences derived from genes with strong promoters, such as the trp gene in E. coli as well as other biosynthetic genes.

Usually, the above described components, comprising a promoter, signal sequence (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extracbromosomal element (eg. plasmids) capable of stable maintenance in a host, such as bacteria. The replicon will have a replication system, thus allowing it to be maintained in a prokaryotic host either for expression or for cloning and amplification. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably contain at least about 10, and more preferably at least about 20 plasmids. Either a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host.

Alternatively, the expression constructs can be integrated into the bacterial genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to the bacterial chromosome that allows the vector to integrate. Integrations appear to result from recombinations between homologous DNA in the vector and the bacterial chromosome. For example, integrating vectors constructed with DNA from various Bacillus strains integrate into the Bacillus chromosome (EP-A-0 127 328). Integrating vectors may also be comprised of bacteriophage or transposon sequences.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of bacterial strains that have been transformed. Selectable markers can be expressed in the bacterial host and may include genes which render bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin (neomycin), and tetracycline [Davies et al. (1978) Annu. Rev. Microbiol. 32:469]. Selectable markers may also include biosynthetic genes, such as those in the histidine, tryptophan, and leucine biosynthetic pathways.

Alternatively, some of the above described components can be put together in transformation vectors. Transformation vectors are usually comprised of a selectable market that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extra-chromosomal replicons or integrating vectors, have been developed for transformation into many bacteria. For example, expression vectors have been developed for, inter alia, the following bacteria: Bacillus subtilis [Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541], Escherichia coli [Shimatake et al. (1981) Nature 292:128; Amann et al. (1985) Gene 40:183; Studier et al. (1986) J. Mol. Biol. 189:113; EP-A-0 036 776,EP-A-0 136 829 and EP-A-0 136 907], Streptococcus cremoris [Powell et al. (1988) Appl. Environ. Microbiol. 54:655]; Streptococcus lividans [Powell et al. (1988) Appl. Environ. Microbiol. 54:655], Streptomyces lividans [U.S. Pat. No. 4,745,056].

Methods of introducing exogenous DNA into bacterial hosts are well-known in the art, and usually include either the transformation of bacteria treated with CaCl₂ or other agents, such as divalent cations and DMSO. DNA can also be introduced into bacterial cells by electroporation. Transformation procedures usually vary with the bacterial species to be transformed. See eg. [Masson et al. (1989) FEMS Microbiol. Lett. 60:273; Palva et al. (1982) Proc. Natl. Acad. Sci. USA 79:5582; EP-A-0 036 259 and EP-A-0 063 953; WO 84/04541, Bacillus], [Miller et al. (1988) Proc. Natl. Acad. Sci. 85:856; Wang et al. (1990) J. Bacteriol. 172:949, Campylobacter], [Cohen et al. (1973) Proc. Natl. Acad. Sci. 69:2110; Dower et al. (1988) Nucleic Acids Res. 16:6127; Kushner (1978) “An improved method for transformation of Escherichia coli with ColE1-derived plasmids. In Genetic Engineering: Proceedings of the International Symposium on Genetic Engineering (eds. H. W. Boyer and S. Nicosia); Mandel et al. (1970) J. Mol. Biol. 53:159; Taketo (1988) Biochim. Biophys. Acta 949:318; Escherichia], [Chassy et al. (1987) FEMS Microbiol. Lett. 44:173 Lactobacillus]; [Fiedler et al. (1988) Anal. Biochem 170:38, Pseudomonas]; [Augustin et al. (1990) FEMS Microbiol. Lett. 66:203, Staphylococcus], [Barany et al. (1980) J. Bacterial. 144:698; Harlander (1987) “Transformation of Streptococcus lactis by electroporation, in: Streptococcal Genetics (ed. J. Ferretti and R. Curtiss III); Perry et al. (1981) Infect. Immun. 32:1295; Powell et al. (1988) Appl. Environ. Microbial. 54:655; Somkuti et al. (1987) Proc. 4th Evr. Cong. Biotechnology 1:412, Streptococcus].

v. Yeast Expression

Yeast expression systems are also known to one of ordinary skill in the art. A yeast promoter is any DNA sequence capable of binding yeast RNA polymerase and initiating the downstream (3′) transcription of a coding sequence (eg. structural gene) into mRNA. A promoter will have a transcription initiation region which is usually placed proximal to the 5′ end of the coding sequence. This transcription initiation region usually includes an RNA polymerase binding site (the “TATA Box”) and a transcription initiation site. A yeast promoter may also have a second domain called an upstream activator sequence (UAS), which, if present, is usually distal to the structural gene. The UAS permits regulated (inducible) expression. Constitutive expression occurs in the absence of a UAS. Regulated expression may be either positive or negative, thereby either enhancing or reducing transcription.

Yeast is a fermenting organism with an active metabolic pathway, therefore sequences encoding enzymes in the metabolic pathway provide particularly useful promoter sequences. Examples include alcohol dehydrogenase (ADH) (EP-A-0 284 044), enolase, glucokinase, glucose-6-phosphate isomerase, glyceraldehyde-3-phosphate-dehydrogenase (GAP or GAPDH), hexokinase, phosphofructokinase, 3-phosphoglycerate mutase, and pyruvate kinase (PyK) (EPO-A-0 329 203). The yeast PH05 gene, encoding acid phosphatase, also provides useful promoter sequences [Myanohara et al. (1983) Proc. Natl. Acad. Sci. USA 80:1].

In addition, synthetic promoters which do not occur in nature also function as yeast promoters. For example, UAS sequences of one yeast promoter maybe joined with the transcription activation region of another yeast promoter, creating a synthetic hybrid promoter. Examples of such hybrid promoters include the ADH regulatory sequence linked to the GAP transcription activation region (U.S. Pat. Nos. 4,876,197 and 4,880,734). Other examples of hybrid promoters include promoters which consist of the regulatory sequences of either the ADH2, GAL4, GAL10, OR PH05 genes, combined with the transcriptional activation region of a glycolytic enzyme gene such as GAP or PyK (EP-A-0 164 556). Furthermore, a yeast promoter can include naturally occurring promoters of non-yeast origin that have the ability to bind yeast RNA polymerase and initiate transcription. Examples of such promoters include, inter alia, [Cohen et al. (1980) Proc. Natl. Acad. Sci. USA 77:1078; Henikoff et al. (1981) Nature 283:835; Hollenberg et al. (1981) Curr. Topics Microbiol. Immunol. 96:119; Hollenberg et al. (1979) “The Expression of Bacterial Antibiotic Resistance Genes in the Yeast Saccharomyces cerevisiae,” in: Plasmids of Medical, Environmental and Commercial Importance (eds. K. N. Timmis and A. Publer); Mercerau-Puigalon et al. (1980) Gene 11:163; Panthier et al. (1980) Curr. Genet. 2:109;].

A DNA molecule may be expressed intracellularly in yeast. A promoter sequence may be directly linked with the DNA molecule, in which case the first amino acid at the N-terminus of the recombinant protein will always be a methionine, which is encoded by the ATG start codon. If desired, methionine at the N-terminus may be cleaved from the protein by in vitro incubation with cyanogen bromide.

Fusion proteins provide an alternative for yeast expression systems, as well as in mammalian, baculovirus, and bacterial expression systems. Usually, a DNA sequence encoding the N-terminal portion of an endogenous yeast protein, or other stable protein, is fused to the 5′ end of heterologous coding sequences. Upon expression, this construct will provide a fusion of the two amino acid sequences. For example, the yeast or human superoxide dismutase (SOD) gene, can be linked at the 5′ terminus of a foreign gene and expressed in yeast. The DNA sequence at the junction of the two amino acid sequences may or may not encode a cleavable site. See eg. EP-A-0 196 056. Another example is a ubiquitin fusion protein. Such a fusion protein is made with the ubiquitin region that preferably retains a site for a processing enzyme (eg. ubiquitin-specific processing protease) to cleave the ubiquitin from the foreign protein. Through this method, therefore, native foreign protein can be isolated (eg. WO88/024066).

Alternatively, foreign proteins can also be secreted from the cell into the growth media by creating chimeric DNA molecules that encode a fusion protein comprised of a leader sequence fragment that provide for secretion in yeast of the foreign protein. Preferably, there are processing sites encoded between the leader fragment and the foreign gene that can be cleaved either in vivo or in vitro. The leader sequence fragment usually encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell.

DNA encoding suitable signal sequences can be derived from genes for secreted yeast proteins, such as the yeast invertase gene (EP-A-0 012 873; JPO. 62,096,086) and the A-factor gene (U.S. Pat. No. 4,588,684). Alternatively, leaders of non-yeast origin, such as an interferon leader, exist that also provide for secretion in yeast (EP-A-0 060 057).

A preferred class of secretion leaders are those that employ a fragment of the yeast alpha-factor gene, which contains both a “pre” signal sequence, and a “pro” region. The types of alpha-factor fragments that can be employed include the full-length pre-pro alpha factor leader (about 83 amino acid residues) as well as truncated alpha-factor leaders (usually about 25 to about 50 amino acid residues) (U.S. Pat. Nos. 4,546,083 and 4,870,008; EP-A-0 324 274). Additional leaders employing an alpha-factor leader fragment that provides for secretion include hybrid alpha-factor leaders made with a presequence of a first yeast, but a pro-region from a second yeast alphafactor. (eg. see WO 89/02463.)

Usually, transcription termination sequences recognized by yeast are regulatory regions located 3′ to the translation stop codon, and thus together with the promoter flank the coding sequence. These sequences direct the transcription of an mRNA which can be translated into the polypeptide encoded by the DNA. Examples of transcription terminator sequence and other yeast-recognized termination sequences, such as those coding for glycolytic enzymes.

Usually, the above described components, comprising a promoter, leader (if desired), coding sequence of interest, and transcription termination sequence, are put together into expression constructs. Expression constructs are often maintained in a replicon, such as an extrachromosomal element (eg. plasmids) capable of stable maintenance in a host, such as yeast or bacteria. The replicon may have two replication systems, thus allowing it to be maintained, for example, in yeast for expression and in a prokaryotic host for cloning and amplification. Examples of such yeast-bacteria shuttle vectors include YEp24 [Botstein et al. (1979) Gene 8:17-24], pCl/1 [Brake et al. (1984) Proc. Natl. Acad. Sci USA 81:4642-4646], and YRp17 (Stinchcomb et al. (1982) J. Mol. Biol. 158:157]. In addition, a replicon may be either a high or low copy number plasmid. A high copy number plasmid will generally have a copy number ranging from about 5 to about 200, and usually about 10 to about 150. A host containing a high copy number plasmid will preferably have at least about 10, and more preferably at least about 20. Enter a high or low copy number vector may be selected, depending upon the effect of the vector and the foreign protein on the host. See eg. Brake et al., supra.

Alternatively, the expression constructs can be integrated into the yeast genome with an integrating vector. Integrating vectors usually contain at least one sequence homologous to a yeast chromosome that allows the vector to integrate, and preferably contain two homologous sequences flanking the expression construct. Integrations appear to result from recombinations between homologous DNA in the vector and the yeast chromosome [Orr-Weaver et al. (1983) Methods in Enzymol. 101:228-2451. An integrating vector may be directed to a specific locus in yeast by selecting the appropriate homologous sequence for inclusion in the vector. See Orr-Weaver et al., supra. One or more expression construct may integrate, possibly affecting levels of recombinant protein produced [Rine et al. (1983) Proc. Natl. Acad. Sci. USA 80:6750]. The chromosomal sequences included in the vector can occur either as a single segment in the vector, which results in the integration of the entire vector, or two segments homologous to adjacent segments in the chromosome and flanking the expression construct in the vector, which can result in the stable integration of only the expression construct.

Usually, extrachromosomal and integrating expression constructs may contain selectable markers to allow for the selection of yeast strains that have been transformed. Selectable markers may include biosynthetic genes that can be expressed in the yeast host, such as ADE2, HIS4, LEU2, TRP1, and ALG7, and the G418 resistance gene, which confer resistance in yeast cells to tunicamycin and G418, respectively. In addition, a suitable selectable marker may also provide yeast with the ability to grow in the presence of toxic compounds, such as metal. For example, the presence of CUP1 allows yeast to grow in the presence of copper ions [Butt et al. (1987) Microbiol, Rev. 51:351].

Alternatively, some of the above described components can be put together into transformation vectors. Transformation vectors are usually comprised of a selectable marker that is either maintained in a replicon or developed into an integrating vector, as described above.

Expression and transformation vectors, either extrachromosomal replicons or integrating vectors, have been developed for transformation into many yeasts. For example, expression vectors have been developed for, inter alia, the following yeasts:Candida albicans [Kurtz, et at. (1986) Mol. Cell. Biol. 6:142], Candida maltosa [Kunze, et at. (1985) J. Basic Microbiol, 25:141]. Hansenula polymorpha [Gleeson, et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302], Kluyveromyces fragilis [Das, et al. (1984) J. Bacteriol. 158:1165], Kluyveromyces lactis [De Louvencourt et al. (1983) J. Bacteriol. 154:737; Van den Berg et al. (1990) Bio/Technology 8:135], Pichia guillerimondii [Kunze et al. (1985) J. Basic Microbiol. 25:141], Pichia pastoris [Cregg, et al. (1985) Mol. Cell. Biol. 5:3376; U.S. Pat. Nos. 4,837,148 and 4,929,555], Saccharomyces cerevisiae [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1929; Ito et al. (1983) J. Bacteriol. 153:163], Schizosaccharomyces pombe [Beach and Nurse (1981) Nature 300:706], and Yarrowia lipolytica [Davidow, et al. (1985) Curr. Genet. 10:380471 Gaillardin, et al. (1985) Curr. Genet. 10:49].

Methods of introducing exogenous DNA into yeast hosts are well-known in the art, and usually include either the transformation of spheroplasts or of intact yeast cells treated with alkali cations. Transformation procedures usually vary with the yeast species to be transformed. See eg. [Kurtz et al. (1986) Mol. Cell. Biol. 6:142; Kunze et al. (1985) J. Basic Microbiol. 25:141; Candida]; [Gleeson et al. (1986) J. Gen. Microbiol. 132:3459; Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302; Hansenula]; [Das et al. (1984) J. Bacterial. 158:1165; De Louvencourt et al. (1983) J. Bacteriol. 154:1165; Van den Berg et al. (1990) Bio/Technology 8:135; Kluyveromyces]; [Cregg et at. (1985) Mol. Cell. Biol. 5:3376; Kunze et al. (1985) J. Basic Microbiol. 25:141; U.S. Pat. Nos. 4,837,148 and 4,929,555; Pichia]; [Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75;1929; Ito et al. (1983) J. Bacteriol. 153:163 Saccharomyces]; [Beach and Nurse (1981) Nature 300:706; Schizosaccbaromyces]; [Davidow et al. (1985) Curr. Genet. 10:39; Gaillardin et al. (1985) Curr. Genet. 10:49; Yarrowia].

Antibodies

As used herein, the term “antibody” refers to a polypeptide or group of polypeptides composed of at least one antibody combining site. An “antibody combining site” is the three-dimensional binding space with an internal surface shape and charge distribution complementary to the features of an epitope of an antigen, which allows a binding of the antibody with the antigen. “Antibody” includes, for example, vertebrate antibodies, hybrid antibodies, chimeric antibodies, humanised antibodies, altered antibodies, univalent antibodies, Fab proteins, and single domain antibodies.

Antibodies against the proteins of the invention are useful for affinity chromatography, immunoassays, and distinguishing/identifying Neisseria proteins.

Antibodies to the proteins of the invention, both polyclonal and monoclonal, may be prepared by conventional methods. In general, the protein is first used to immunize a suitable animal, preferably a mouse, rat, rabbit or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat antibodies. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 μg/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund's incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization. Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25° C. for one hour, followed by incubating at 4° C. for 2-18 hours. The serum is recovered by centrifugation (eg. 1,000g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits.

Monoclonal antibodies are prepared using the standard method of Kohler & Milstein [Nature (1975) 256:495-96], or a modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate or well coated with the protein antigen. B-cells expressing membrane-bound immunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas, and are cultured in a selective medium (eg. hypoxanthine, aminopterin, thymidine medium, “HAT”). The resulting hybridomas are plated by limiting dilution, and are assayed for production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected MAb-secreting hybridomas are then cultured either in vitro (eg. in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice).

If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly ³²P and ¹²⁵I), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3′,5,5′-tetramethylbenzidine (TMB) to a blue pigment, quantifiable with a spectrophotometer. “Specific binding partner” refers to a protein capable of binding a ligand molecule with high specificity, as for example in the case of an antigen and a monoclonal antibody specific therefor. Other specific binding partners include biotin and avidin or streptavidin, IgG and protein A, and the numerous receptor-ligand couples known in the art. It should be understood that the above description is not meant to categorize the various labels into distinct classes, as the same label may serve in several different modes. For example, ¹²⁵I may serve as a radioactive label or as an electron-dense reagent. HRP may serve as enzyme or as antigen for a MAb. Further, one may combine various labels for desired effect. For example, MAbs and avidin also require labels in the practice of this invention: thus, one might label a MAb with biotin, and detect its presence with avidin labeled with ¹²⁵I, or with an anti-biotin MAb labeled with HRP. Other permutations and possibilities will be readily apparent to those of ordinary skill in the art, and are considered as equivalents within the scope of the instant invention.

Pharmaceutical Compositions

Pharmaceutical compositions can comprise either polypeptides, antibodies, or nucleic acid of the invention. The pharmaceutical compositions will comprise a therapeutically effective amount of either polypeptides, antibodies, or polynucleotides of the claimed invention.

The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased body temperature. The precise effective amount for a subject will depend upon the subject's size and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount in advance. However, the effective amount for a given situation can be determined by routine experimentation and is within the judgement of the clinician.

For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent, such as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive virus particles. Such carriers are well known to those of ordinary skill in the art.

Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).

Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles. Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier.

Delivery Methods

Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals; in particular, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Vaccines

Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection).

Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with “pharmaceutically acceptable carriers,” which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Additionally, these carriers may function as immunostimulating agents (“adjuvants”). Furthermore, the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, etc. pathogens.

Preferred adjuvants to enhance effectiveness of the composition include, but are not limited to: (1) aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc; (2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (see below) or bacterial cell wall components), such as for example (a) MF59™ (WO 90/14837; Chapter 10 in Vaccine design: the subunit and adjuvant approach, eds. Powell & Newman, Plenum Press 1995), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionally containing various amounts of MTP-PE (see below), although not required) formulated into submicron particles using a microfluidizer such as Model 110Y microfluidizer (Microfluidics, Newton, Mass.), (b) SAF, containing 10% Squalane, 0.4% Tween 80, 5% pluronic-blocked polymer L121, and thr-MDP (see below) either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) Ribi™ adjuvant system (RAS), (Ribi Immunochem, Hamilton, Mont.) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (Detox™); (3) saponin adjuvants, such as Stimulon™ (Cambridge Bioscience, Worcester, Mass.) may be used or particles generated therefrom such as ISCOMs (immunostimulating complexes); (4) Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (5) cytokines, such as interleukins (eg. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (eg. gamma interferon), macrophage colony stimulating factor (M-CSF), tumor necrosis factor (TNF), etc; and (6) other substances that act as immunostimulating agents to enhance the effectiveness of the composition. Alum and MF59™ are preferred.

As mentioned above, muramyl peptides include, but are not limited to, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuram yl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), etc.

The immunogenic compositions (eg. the immunising antigen/immunogen/polypeptide/protein/nucleic acid, pharmaceutically acceptable carrier, and adjuvant) typically will contain diluents, such as water, saline, glycerol, ethanol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.

Typically, the immunogenic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. The preparation also may be emulsified or encapsulated in liposomes for enhanced adjuvant effect, as discussed above under pharmaceutically acceptable carriers.

Immunogenic compositions used as vaccines comprise an immunologically effective amount of the antigenic or immunogenic polypeptides, as well as any other of the above-mentioned components, as needed. By “immunologically effective amount”, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, the taxonomic group of individual to be treated (eg. nonhuman primate, primate, etc.), the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.

The immunogenic compositions are conventionally administered parenterally, eg. by injection, either subcutaneously, intramuscularly, or transdermally/transcutaneously (eg. WO98/20734). Additional formulations suitable for other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Dosage treatment may be a single dose schedule or a multiple dose schedule. The vaccine may be administered in conjunction with other immunoregulatory agents.

As an alternative to protein-based vaccines, DNA vaccination may be used [eg. Robinson & Torres (1997) Seminars in Immunol 9:271-283; Donnelly et al. (1997) Annu Rev Immunol 15:617-648; later herein].

Gene Delivery Vehicles

Gene therapy vehicles for delivery of constructs including a coding sequence of a therapeutic of the invention, to be delivered to the mammal for expression in the mammal, can be administered either locally or systemically. These constructs can utilize viral or non-viral vector approaches in in vivo or ex vivo modality. Expression of such coding sequence can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence in vivo can be either constitutive or regulated.

The invention includes gene delivery vehicles capable of expressing the contemplated nucleic acid sequences. The gene delivery vehicle is preferably a viral vector and, more preferably, a retroviral, adenoviral, adeno-associated viral (AAV), herpes viral, or alphavirus vector. The viral vector can also be an astrovirus, coronavirus, orthomyxovirus, papovavirus, paramyxovirus, parvovirus, picornavirus, poxvirus, or togavirus viral vector. See generally, Jolly (1994) Cancer Gene Therapy 1:51-64; Kimura (1994) Human Gene Therapy 5:845-852; Connelly (1995) Human Gene Therapy 6:185-193; and Kaplitt (1994) Nature Genetics 6:148-153.

Retroviral vectors are well known in the art and we contemplate that any retroviral gene therapy vector is employable in the invention, including B, C and D type retroviruses, xenotropic retroviruses (for example, NZB-X1, NZB-X2 and NZB9-1 (see O'Neill (1985) J. Virol. 53:160) polytropic retroviruses eg. MCF and MCF-MLV (see Kelly (1983) J. Virol. 45:291), spumaviruses and lentiviruses. See RNA Tumor Viruses, Second Edition, Cold Spring Harbor Laboratory, 1985.

Portions of the retroviral gene therapy vector may be derived from different retroviruses. For example, retrovector LTRs may be derived from a Murine Sarcoma Virus, a TRNA binding site from a Rous Sarcoma Virus, a packaging signal from a Murine Leukemia Virus, and an origin of second strand synthesis from an Avian Leukosis Virus.

These recombinant retroviral vectors may be used to generate transduction competent retroviral vector particles by introducing them into appropriate packaging cell lines (see U.S. Pat. No. 5,591,624). Retrovirus vectors can be constructed for site-specific integration into host cell DNA by incorporation of a chimeric integrase enzyme into the retroviral particle (see WO96/37626). It is preferable that the recombinant viral vector is a replication defective recombinant virus.

Packaging cell lines suitable for use with the above-described retrovirus vectors are well known in the art, are readily prepared (see WO95/30763 and WO92/05266), and can be used to create producer cell lines (also termed vector cell lines or “VCLs”) for the production of recombinant vector particles. Preferably, the packaging cell lines are made from human parent cells (eg. HT1080 cells) or mink parent cell lines, which eliminates inactivation in human serum.

Preferred retroviruses for the construction of retroviral gene therapy vectors include Avian Leukosis Virus, Bovine Leukemia, Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Virus, Murine Sarcoma Virus, Reticuloendotheliosis Virus and Rous Sarcoma Virus. Particularly preferred Murine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe (1976) J Virol 19:19-25), Abelson (ATCC No. VR-999), Friend (ATCC No. VR-245), Graffi, Gross (ATCC Nol VR-590), Kirsten, Harvey Sarcoma Virus and Rauscher (ATCC No. VR-998) and Moloney Murine Leukemia Virus (ATCC No. VR-190). Such retroviruses may be obtained from depositories or collections such as the American Type Culture Collection (“ATCC”) in Rockville, Md. or isolated from known sources using commonly available techniques.

Exemplary known retroviral gene therapy vectors employable in this invention include those described in patent applications GB2200651, EP0415731, EP0345242, EP0334301, WO89/02468; WO89/05349, WO89/09271, WO90/02806, WO90/07936, WO94/03622, WO93/25698, WO93/25234, WO93/11230, WO93/10218, WO91/02805, WO91/02825, WO95/07994, U.S. Pat. Nos. 5,219,740, 4,405,712, 4,861,719, 4,980,289, 4,777,127, 5,591,624. See also Vile (1993) Cancer Res 53:3860-3864; Vile (1993) Cancer Res 53:962-967; Ram (1993) Cancer Res 53 (1993) 83-88; Takamiya (1992) J Neurosci Res 33:493-503; Baba (1993) J Neurosurg 79:729-735; Mann (1983) Cell 33:153; Cane (1984) Proc Natl Acad Sci 81:6349; and Miller (1990) Human Gene Therapy 1.

Human adenoviral gene therapy vectors are also known in the art and employable in this invention, See, for example, Berkner (1988) Biotechniques 6:616 and Rosenfeld (1991) Science 252:431, and WO93/07283, WO93/06223, and WO93/07282. Exemplary known adenoviral gene therapy vectors employable in this invention include those described in the above referenced documents and in WO94/12649, WO93/03769, WO93/19191, WO94/28938, WO95/11984, WO95/00655, WO95/27071, WO95/29993, WO95/34671, WO96/05320, WO94/08026, WO94/11506, WO93/06223, WO94/24299, WO95/14102, WO95/24297, WO95/02697, WO94/28152, WO94/24299, WO95/09241, WO95/25807, WO95/05835, WO94/18922 and WO95/09654. Alternatively, administration of DNA linked to killed adenovirus as described in Curiel (1992) Hum. Gene Ther. 3:147-154 may be employed. The gene delivery vehicles of the invention also include adenovirus associated virus (AAV) vectors. Leading and preferred examples of such vectors for use in this invention are the AAV-2 based vectors disclosed in Srivastava, WO93/09239. Most preferred AAV vectors comprise the two AAV inverted terminal repeats in which the native D-sequences are modified by substitution of nucleotides, such that at least 5 native nucleotides and up to 18 native nucleotides, preferably at least 10 native nucleotides up to 18 native nucleotides, most preferably 10 native nucleotides are retained and the remaining nucleotides of the D-sequence are deleted or replaced with non-native nucleotides. The native D-sequences of the AAV inverted terminal repeats are sequences of 20 consecutive nucleotides in each AAV inverted terminal repeat (ie. there is one sequence at each end) which are not involved in HP formation. The non-native replacement nucleotide may be any nucleotide other than the nucleotide found in the native D-sequence in the same position. Other employable exemplary AAV vectors are pWP-19, pWN-1, both of which are disclosed in Nahreini (1993) Gene 124:257-262. Another example of such an AAV vector is psub201 (see Samulski (1987) J. Virol. 61:3096). Another exemplary AAV vector is the Double-D ITR vector. Construction of the Double-D ITR vector is disclosed in U.S. Pat. No. 5,478,745. Still other vectors are those disclosed in Carter U.S. Pat. No. 4,797,368 and Muzyczka U.S. Pat. No. 5,139,941, Chartejee U.S. Pat. No. 5,474,935, and Kotin WO94/288157. Yet a further example of an AAV vector employable in this invention is SSV9AFABTKneo, which contains the AFP enhancer and albumin promoter and directs expression predominantly in the liver. Its structure and construction are disclosed in Su (1996) Human Gene Therapy 7:463-470. Additional AAV gene therapy vectors are described in U.S. Pat. Nos. 5,354,678, 5,173,414, 5,139,941, and 5,252,479.

The gene therapy vectors of the invention also include herpes vectors. Leading and preferred examples are herpes simplex virus vectors containing a sequence encoding a thymidine kinase polypeptide such as those disclosed in U.S. Pat. No. 5,288,641 and EP0176170 (Roizman). Additional exemplary herpes simplex virus vectors include HFEM/ICP6-LacZ disclosed in WO95/04139 (Wistar Institute), pHSVlac described in Geller (1988) Science 241:1667-1669 and in WO90/09441 and WO92/07945, HSV Us3::pgC-lacZ described in Fink (1992) Human Gene Therapy 3:11-19 and HSV 7134, 2 RH 105 and GAL4 described in EP 0453242 (Breakefield), and those deposited with the ATCC with accession numbers VR-977 and VR-260.

Also contemplated are alpha virus gene therapy vectors that can be employed in this invention. Preferred alpha virus vectors are Sindbis viruses vectors. Togaviruses, Semliki Forest virus (ATCC VR-67; ATCC VR-1247), Middleberg virus (ATCC VR-370), Ross River virus (ATCC VR-373; ATCC VR-1246), Venezuelan equine encephalitis virus (ATCC VR923; ATCC VR-1250; ATCC VR-1249; ATCC VR-532), and those described in U.S. Pat. Nos. 5,091,309, 5,217,879, and WO92/10578. More particularly, those alpha virus vectors described in U.S. Ser. No. 08/405,627, filed Mar. 15, 1995, WO94/21792, WO92/10578, WO95/07994, U.S. Pat. Nos. 5,091,309 and 5,217,879 are employable. Such alpha viruses may be obtained from depositories or collections such as the ATCC in Rockville, Md. or isolated from known sources using commonly available techniques. Preferably, alphavirus vectors with reduced cytotoxicity are used (see U.S. Ser. No. 08/679640).

DNA vector systems such as eukaryotic layered expression systems are also useful for expressing the nucleic acids of the invention. See WO95/07994 for a detailed description of eukaryotic layered expression systems. Preferably, the eukaryotic layered expression systems of the invention are derived from alphavirus vectors and most preferably from Sindbis viral vectors.

Other viral vectors suitable for use in the present invention include those derived from poliovirus, for example ATCC VR-58 and those described in Evans, Nature 339 (1989) 385 and Sabin (1973) J. Biol. Standardization 1:115; rhinovirus, for example ATCC VR-11 10 and those described in Arnold (1990) J Cell Biochem L401; pox viruses such as canary pox virus or vaccinia virus, for example ATCC VR-111 and ATCC VR-2010 and those described in Fisher-Hoch (1989) Proc Natl Acad Sci 86:317; Flexner (1989) Ann NY Acad Sci 569:86, Flexner (1990) Vaccine 8:17; in U.S. Pat. Nos. 4,603,112 and 4,769,330 and WO89/01973; SV40 virus, for example ATCC VR-305 and those described in Mulligan (1979) Nature 277:108 and Madzak (1992) J Gen Virol 73:1533; influenza virus, for example ATCC VR-797 and recombinant influenza viruses made employing reverse genetics techniques as described in U.S. Pat. No. 5,166,057 and in Enami (1990) Proc Natl Acad Sci 87:3802-3805; Enami & Palese (1991) J Virol 65:2711-2713 and Luytjes (1989) Cell 59:110, (see also McMichael (1983) NEI Med 309:13, and Yap (1978) Nature 273:238 and Nature (1979) 277:108); human immunodeficiency virus as described in EP-0386882 and in Buchschacher (1992) J. Virol. 66:2731; measles virus, for example ATCC VR-67 and VR-1247 and those described in EP-0440219; Aura virus, for example ATCC VR-368; Bebaru virus, for example ATCC VR-600 and ATCC VR-1240; Cabassou virus, for example ATCC VR-922; Chikungunya virus, for example ATCC VR-64 and ATCC VR-1241; Fort Morgan Virus, for example ATCC VR-924; Getah virus, for example ATCC VR-369 and ATCC VR-1243; Kyzylagach virus, for example ATCC VR-927; Mayaro virus, for example ATCC VR-66; Mucambo virus, for example ATCC VR-580 and ATCC VR-1244; Ndumu virus, for example ATCC VR-371; Pixuna virus, for example ATCC VR-372 and ATCC VR-1245; Tonate virus, for example ATCC VR-925; Triniti virus, for example ATCC VR-469; Una virus, for example ATCC VR-374; Whataroa virus, for example ATCC VR-926; Y-62-33 virus, for example ATCC VR-375; O'Nyong virus, Eastern encephalitis virus, for example ATCC VR-65 and ATCC VR-1242; Western encephalitis virus, for example ATCC VR-70, ATCC VR-1251, ATCC VR-622 and ATCC VR-1252; and coronavirus, for example ATCC VR-740 and those described in Hamre (1966) Proc Soc Exp Biol Med 121:190.

Delivery of the compositions of this invention into cells is not limited to the above mentioned viral vectors. Other delivery methods and media may be employed such as, for example, nucleic acid expression vectors, polycationic condensed DNA linked or unlinked to killed adenovirus alone, for example see U.S. Ser. No. 08/366,787, filed Dec. 30, 1994 and Curiel (1992) Hum Gene Ther 3:147-154 ligand linked DNA, for example see Wu (1989) J Biol Chem 264:16985-16987, eucaryotic cell delivery vehicles cells, for example see U.S. Ser. No. 08/240,030, filed May 9, 1994, and U.S. Ser. No. 08/404,796, deposition of photopolymerized hydrogel materials, hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655, ionizing radiation as described in U.S. Pat. No. 5,206,152 and in WO92/11033, nucleic charge neutralization or fusion with cell membranes. Additional approaches are described in Philip (1994) Mol Cell Biol 14:2411-2418 and in Woffendin (1994) Proc Natl Acad Sci 91:1581-1585.

Particle mediated gene transfer may be employed, for example see U.S. Ser. No. 60/023,867. Briefly, the sequence can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, as described in Wu & Wu (1987) J. Biol. Chem. 262:4429-4432, insulin as described in Hucked (1990) Biochem Pharmacol 40:253-263, galactose as described in Plank (1992) Bioconjugate Chem 3:533-539, lactose or transferrin.

Naked DNA may also be employed. Exemplary naked DNA introduction methods are described in WO 90/11092 and U.S. Pat. No. 5,580,859. Uptake efficiency may be improved using biodegradable latex beads. DNA coated latex beads are efficiently transported into cells after endocytosis initiation by the beads. The method may be improved further by treatment of the beads to increase hydrophobicity and thereby facilitate disruption of the endosome and release of the DNA into the cytoplasm.

Liposomes that can act as gene delivery vehicles are described in U.S. Pat. No. 5,422,120, WO95/13796, WO94/23697, WO91/14445 and EP-524,968. As described in U.S. Ser. No. 60/023,867, on non-viral delivery, the nucleic acid sequences encoding a polypeptide can be inserted into conventional vectors that contain conventional control sequences for high level expression, and then be incubated with synthetic gene transfer molecules such as polymeric DNA-binding cations like polylysine, protamine, and albumin, linked to cell targeting ligands such as asialoorosomucoid, insulin, galactose, lactose, or transferrin. Other delivery systems include the use of liposomes to encapsulate DNA comprising the gene under the control of a variety of tissue-specific or ubiquitously-active promoters. Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in Woffendin et al (1994) Proc. Natl. Acad. Sci. USA 91(24):11581-11585. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun, as described in U.S. Pat. No. 5,149,655; use of ionizing radiation for activating transferred gene, as described in U.S. Pat. No. 5,206,152 and WO92/11033.

Exemplary liposome and polycationic gene delivery vehicles are those described in U.S. Pat. Nos. 5,422,120 and 4,762,915; in WO 95/13796; WO94/23697; and WO91/14445; in EP-0524968; and in Stryer, Biochemistry, pages 236-240 (1975) W.H. Freeman, San Francisco; Szoka (1980) Biochem Biophys Acta 600:1; Bayer (1979) Biochem Biophys Acta 550:464; Rivnay (1987) Meth Enzymol 149:119; Wang (1987) Proc Natl Acad Sci 84:7851; Plant (1989) Anal Biochem 176:420.

A polynucleotide composition can comprises therapeutically effective amount of a gene therapy vehicle, as the term is defined above. For purposes of the present invention, an effective dose will be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.

Delivery Methods

Once formulated, the polynucleotide compositions of the invention can be administered (1) directly to the subject; (2) delivered ex vivo, to cells derived from the subject; or (3) in vitro for expression of recombinant proteins. The subjects to be treated can be mammals or birds. Also, human subjects can be treated.

Direct delivery of the compositions will generally be accomplished by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications (eg. see WO98/20734), needles, and gene guns or hyposprays. Dosage treatment may be a single dose schedule or a multiple dose schedule.

Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known in the art and described in eg. WO93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hem atopoetic, lymph cells, macrophages, dendritic cells, or tumor cells.

Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished by the following procedures, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well known in the art.

Polynucleotide and Polypeptide Pharmaceutical Compositions

In addition to the pharmaceutically acceptable carriers and salts described above, the following additional agents can be used with polynucleotide and/or polypeptide compositions.

A. Polypeptides

One example are polypeptides which include, without limitation: asioloorosomucoid (ASOR); transferrin; asialoglycoproteins; antibodies; antibody fragments; ferritin; interleukins; interferons, granulocyte, macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), stem cell factor and erythropoietin. Viral antigens, such as envelope proteins, can also be used. Also, proteins from other invasive organisms, such as the 17 amino acid peptide from the circumsporozoite protein of plasmodium falciparum known as RII.

B. Hormones, Vitamins, etc.

Other groups that can be included are, for example: hormones, steroids, androgens, estrogens, thyroid hormone, or vitamins, folic acid.

C. Polyalkylenes, Polysaccharides, etc.

Also, polyalkylene glycol can be included with the desired polynucleotides/polypeptides. In a preferred embodiment, the polyalkylene glycol is polyethlylene glycol. In addition, mono-, di-, or polysaccharides can be included. In a preferred embodiment of this aspect, the polysaccharide is dextran or DEAE-dextran. Also, chitosan and poly(lactide-co-glycolide)

D. Lipids, and Liposomes

The desired polynucleotidelpolypeptide can also be encapsulated in lipids or packaged in liposomes prior to delivery to the subject or to cells derived therefrom.

Lipid encapsulation is generally accomplished using liposomes which are able to stably bind or entrap and retain nucleic acid. The ratio of condensed polynucleotide to lipid preparation can vary but will generally be around 1:1 (mg DNA:micromoles lipid), or more of lipid. For a review of the use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) Biochim. Biophys. Acta. 1097:1-17; Straubinger (1983) Meth. Enzymol. 101:512-527.

Liposomal preparations for use in the present invention include cationic (positively charged), anionic (negatively charged) and neutral preparations. Cationic liposomes have been shown to mediate intracellular delivery of plasmid DNA (Feigner (1987) Proc. Natl. Acad. Sci. USA 84:7413-7416); mRNA (Malone (1989) Proc. Natl. Acad. Sci. USA 86:6077-6081); and purified transcription factors (Debs (1990) J. Biol. Chem. 265:10189-10192), in functional form.

Cationic liposomes are readily available. For example, N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes are available under the trademark Lipofectin, from GIBCO BRL, Grand Island, N.Y. (See, also, Feigner supra). Other commercially available liposomes include transfectace (DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes can be prepared from readily available materials using techniques well known in the art. See, eg. Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; WO90/11092 for a description of the synthesis of DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.

Similarly, anionic and neutral liposomes are readily available, such as from Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using readily available materials. Such materials include phosphatidyl choline, cholesterol, phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC), dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE), among others. These materials can also be mixed with the DOTMA and DOTAP starting materials in appropriate ratios. Methods for making liposomes using these materials are well known in the art.

The liposomes can comprise multilammelar vesicles (MLVs), small unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs). The various liposome-nucleic acid complexes are prepared using methods known in the art. See eg. Straubinger (1983) Meth. Immunol. 101:512-527; Szoka (1978) Proc. Natl. Acad. Sci. USA 75:4194-4198; Papahadjopoulos (1975) Biochim. Biophys. Acta 394:483; Wilson (1979) Cell 17:77); Deamer & Bangham (1976) Biochim. Biophys. Acta 443:629; Ostro (1977) Biochem. Biophys. Res. Commun. 76:836; Fraley (1979) Proc. Natl. Acad. Sci. USA 76:3348); Enoch & Strittmatter (1979) Proc. Natl. Acad. Sci. USA 76:145; Fraley (1980) J. Biol. Chem. (1980) 255:10431; Szoka & Papahadjopoulos (1978) Proc. Natl. Acad. Sci. USA 75:145; and Schaefer-Ridder (1982) Science 215:166.

E. Lipoproteins

In addition, lipoproteins can be included with the polynucleotide/polypeptide to be delivered. Examples of lipoproteins to be utilized include: chylomicrons, HDL, IDL, LDL, and VLDL. Mutants, fragments, or fusions of these proteins can also be used. Also, modifications of naturally occurring lipoproteins can be used, such as acetylated LDL. These lipoproteins can target the delivery of polynucleotides to cells expressing lipoprotein receptors. Preferably, if lipoproteins are including with the polynucleotide to be delivered, no other targeting ligand is included in the composition.

Naturally occurring lipoproteins comprise a lipid and a protein portion. The protein portion are known as apoproteins. At the present, apoproteins A, B, C, D, and E have been isolated and identified. At least two of these contain several proteins, designated by Roman numerals, AI, AII, AIV; CI, CII, CIII.

A lipoprotein can comprise more than one apoprotein. For example, naturally occurring chylomicrons comprises of A, B, C & E, over time these lipoproteins lose A and acquire C & E. VLDL comprises A, B, C & E apoproteins, LDL comprises apoprotein B; and HDL comprises apoproteins A, C, & E.

The amino acid of these apoproteins are known and are described in, for example, Breslow (1985) Annu Rev. Biochem 54:699; Law (1986) Adv. Exp Med. Biol. 151:162; Chen (1986) J Biol Chem 261:12918; Kane (1980) Proc Natl Acad Sci USA 77:2465; and Utermann (1984) Hum Genet 65:232.

Lipoproteins contain a variety of lipids including, triglycerides, cholesterol (free and esters), and phospholipids, The composition of the lipids varies in naturally occurring lipoproteins. For example, chylomicrons comprise mainly triglycerides. A more detailed description of the lipid content of naturally occurring lipoproteins can be found, for example, in Meth. Enzymol. 128 (1986). The composition of the lipids are chosen to aid in conformation of the apoprotein for receptor binding activity. The composition of lipids can also be chosen to facilitate hydrophobic interaction and association with the polynucleotide binding molecule.

Naturally occurring lipoproteins can be isolated from serum by ultracentrifugation, for instance. Such methods are described in Meth. Enzymol. (supra); Pitas (1980) J. Biochem. 255:5454-5460 and Mahey (1979) J Clin. Invest 64:743-750. Lipoproteins can also be produced by in vitro or recombinant methods by expression of the apoprotein genes in a desired host cell. See, for example, Atkinson (1986) Annu Rev Biophys Chem 15:403 and Radding (1958) Biochim Biophys Acta 30: 443. Lipoproteins can also be purchased from commercial suppliers, such as Biomedical Techniologies, Inc., Stoughton, Mass., USA. Further description of lipoproteins can be found in Zuckermann et al. PCT/US97/14465.

F. Polycationic Agents

Polycationic agents can be included, with or without lipoprotein, in a composition with the desired polynucleotide/polypeptide to be delivered.

Polycationic agents, typically, exhibit a net positive charge at physiological relevant pH and are capable of neutralizing the electrical charge of nucleic acids to facilitate delivery to a desired location. These agents have both in vitro, ex vivo, and in vivo applications. Polycationic agents can be used to deliver nucleic acids to a living subject either intramuscularly, subcutaneously, etc.

The following are examples of useful polypeptides as polycationic agents: polylysine, polyarginine, polyornithine, and protamine. Other examples include histones, protamines, human serum albumin, DNA binding proteins, non-histone chromosomal proteins, coat proteins from DNA viruses, such as (X174, transcriptional factors also contain domains that bind DNA and therefore may be useful as nucleic aid condensing agents. Briefly, transcriptional factors such as C/CEBP, cjun, c-fos, AP-1, AP-2, AP-3, CPF, Prot-1, Sp-1, Oct-1, Oct-2, CREP, and TFIID contain basic domains that bind DNA sequences.

Organic polycationic agents include: spermine, spermidine, and purtrescine.

The dimensions and of the physical properties of a polycationic agent can be extrapolated from the list above, to construct other polypeptide polycationic agents or to produce synthetic polycationic agents.

Synthetic polycationic agents which are useful include, for example, DEAE-dextran, polybrene. Lipofectin™, and lipofectAMINE™ are monomers that form polycationic complexes when combined with polynucleotides/polypeptides.

Immunodiagnostic Assays

Neisseria antigens of the invention can be used in immunoassays to detect antibody levels (or, conversely, anti-Neisseria antibodies can be used to detect antigen levels). Immunoassays based on well defined, recombinant antigens can be developed to replace invasive diagnostics methods. Antibodies to Neisseria proteins within biological samples, including for example, blood or serum samples, can be detected. Design of the immunoassays is subject to a great deal of variation, and a variety of these are known in the art. Protocols for the immunoassay may be based, for example, upon competition, or direct reaction, or sandwich type assays. Protocols may also, for example, use solid supports, or may be by immunoprecipitation. Most assays involve the use of labeled antibody or polypeptide; the labels may be, for example, fluorescent, chemiluminescent, radioactive, or dye molecules. Assays which amplify the signals from the probe are also known; examples of which are assays which utilize biotin and avidin, and enzyme-labeled and mediated immunoassays, such as ELISA assays.

Kits suitable for immunodiagnosis and containing the appropriate labeled reagents are constructed by packaging the appropriate materials, including the compositions of the invention, in suitable containers, along with the remaining reagents and materials (for example, suitable buffers, salt solutions, etc.) required for the conduct of the assay, as well as suitable set of assay instructions.

Nucleic Acid Hybridisation

“Hybridization” refers to the association of two nucleic acid sequences to one another by hydrogen bonding. Typically, one sequence will be fixed to a solid support and the other will be free in solution. Then, the two sequences will be placed in contact with one another under conditions that favor hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase sequence to the solid support (Denhardt's reagent or BLOTTO); concentration of the sequences; use of compounds to increase the rate of association of sequences (dextran sulfate or polyethylene glycol); and the stringency of the washing conditions following hybridization. See Sambrook et al. [supral Volume 2, chapter 9, pages 9.47 to 9.57.

“Stringency” refers to conditions in a hybridization reaction that favor association of very similar sequences over sequences that differ. For example, the combination of temperature and salt concentration should be chosen that is approximately 120 to 200° C. below the calculated Tm of the hybrid under study. The temperature and salt conditions can often be determined empirically in preliminary experiments in which samples of genomic DNA immobilized on filters are hybridized to the sequence of interest and then washed under conditions of different stringencies. See Sambrook et al. at page 9.50.

Variables to consider when performing, for example, a Southern blot are (1) the complexity of the DNA being blotted and (2) the homology between the probe and the sequences being detected. The total amount of the fragment(s) to be studied can vary a magnitude of 10, from 0.1 to lug for a plasmid or phage digest to 10⁻⁹ to 10⁻⁸ g for a single copy gene in a highly complex eukaryotic genome. For lower complexity polynucleotides, substantially shorter blotting, hybridization, and exposure times, a smaller amount of starting polynucleotides, and lower specific activity of probes an be used. For example, a single-copy yeast gene can be detected with an exposure time of only 1 hour starting with 1 μg of yeast DNA, blotting for two hours, and hybridizing for 4-8 hours with a probe of 10⁸ cpm/μg. For a single-copy mammalian gene a conservative approach would start with 10 μg of DNA, blot overnight, and hybridize overnight in the presence of 10% dextran sulfate using a probe of greater than 10⁸ cpm/μg, resulting in an exposure time of ˜24 hours.

Several factors can affect the melting temperature (Tm) of a DNA-DNA hybrid between the probe and the fragment of interest, and consequently, the appropriate conditions for hybridization and washing. In many cases the probe is not 100% homologous to the fragment. Other commonly encountered variables include the length and total G+C content of the hybridizing sequences and the ionic strength and form amide content of the hybridization buffer. The effects of all of these factors can be approximated by a single equation: Tm=81+16.6(log₁₀ Ci)+0.4[%(G+C)]0.6(% formamide)−600/n-1.5(% mismatch). where Ci is the salt concentration (monovalent ions) and n is the length of the hybrid in base pairs (slightly modified from Meinkoth & Wahl (1984) Anal. Biochem. 138: 267-284).

In designing a hybridization experiment, some factors affecting nucleic acid hybridization can be conveniently altered. The temperature of the hybridization and washes and the salt concentration during the washes are the simplest to adjust. As the temperature of the hybridization increases (ie. stringency), it becomes less likely for hybridization to occur between strands that are nonhomologous, and as a result, background decreases. If the radiolabeled probe is not completely homologous with the immobilized fragment (as is frequently the case in gene family and interspecies hybridization experiments), the hybridization temperature must be reduced, and background will increase. The temperature of the washes affects the intensity of the hybridizing band and the degree of background in a similar manner. The stringency of the washes is also increased with decreasing salt concentrations.

In general, convenient hybridization temperatures in the presence of 50% formamide are 42° C. for a probe with is 95% to 100% homologous to the target fragment, 37° C for 90% to 95% homology, and 32° C. for 85% to 90% homology. For lower homologies, formamide content should be lowered and temperature adjusted accordingly, using the equation above. If the homology between the probe and the target fragment are not known, the simplest approach is to start with both hybridization and wash conditions which are nonstringent. If non-specific bands or high background are observed after autoradiography, the filter can be washed at high stringency and reexposed. If the time required for exposure makes this approach impractical, several hybridization and/or washing stringencies should be tested in parallel.

Nucleic Acid Probe Assays

Methods such as PCR, branched DNA probe assays, or blotting techniques utilizing nucleic acid probes according to the invention can determine the presence of cDNA or mRNA. A probe is said to “hybridize” with a sequence of the invention if it can form a duplex or double stranded complex, which is stable enough to be detected.

The nucleic acid probes will hybridize to the Neisseria nucleotide sequences of the invention (including both sense and antisense strands). Though many different nucleotide sequences will encode the amino acid sequence, the native Neisseria sequence is preferred because it is the actual sequence present in cells. mRNA represents a coding sequence and so a probe should be complementary to the coding sequence; single-stranded cDNA is complementary to mRNA, and so a cDNA probe should be complementary to the non-coding sequence.

The probe sequence need not be identical to the Neisseria sequence (or its complement)—some variation in the sequence and length can lead to increased assay sensitivity if the nucleic acid probe can form a duplex with target nucleotides, which can be detected. Also, the nucleic acid probe can include additional nucleotides to stabilize the formed duplex, Additional Neisseria sequence may also be helpful as a label to detect the formed duplex. For example, a non-complementary nucleotide sequence may be attached to the 5′ end of the probe, with the remainder of the probe sequence being complementary to a Neisseria sequence. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the a Neisseria sequence in order to hybridize therewith and thereby form a duplex which can be detected.

The exact length and sequence of the probe will depend on the hybridization conditions (e.g. temperature, salt condition etc.). For example, for diagnostic applications, depending on the complexity of the analyte sequence, the nucleic acid probe typically contains at least 10-20 nucleotides, preferably 15-25, and more preferably at least 30 nucleotides, although it may be shorter than this. Short primers generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.

Probes may be produced by synthetic procedures, such as the triester method of Matteucci et al. [J. Am. Chem. Soc. (1981) 103:31853, or according to Urdea et al. [Proc. Natl. Acad. Sci. USA (1983) 80: 7461], or using commercially available automated oligonucleotide synthesizers.

The chemical nature of the probe can be selected according to preference. For certain applications, DNA or RNA are appropriate. For other applications, modifications may be incorporated eg. backbone modifications, such as phosphorothioates or methylphosphonates, can be used to increase in vivo half-life, alter RNA affinity, increase nuclease resistance etc. [eg. see Agrawal & Jyer (1995) Curr Opin Biotechnol 6:12-19; Agrawal (1996) TIBTECH 14:376-387]; analogues such as peptide nucleic acids may also be used [eg. see Corey (1997) TIBTECH 15:224-229; Buchardt et al. (1993) TIBTECH 11:384-386].

Alternatively, the polymerase chain reaction (PCR) is another well-known means for detecting small amounts of target nucleic acid. The assay is described in Mullis et al. [Meth. Enzymol. (1987) 155:335-350] & U.S. Pat. Nos. 4,683,195 & 4,683,202. Two “primer” nucleotides hybridize with the target nucleic acids and are used to prime the reaction. The primers can comprise sequence that does not hybridize to the sequence of the amplification target (or its complement) to aid with duplex stability or, for example, to incorporate a convenient restriction site. Typically, such sequence will flank the desired Neisseria sequence.

A thermostable polymerase creates copies of target nucleic acids from the primers using the original target nucleic acids as a template. After a threshold amount of target nucleic acids are generated by the polymerase, they can be detected by more traditional methods, such as Southern blots. When using the Southern blot method, the labelled probe will hybridize to the Neisseria sequence (or its complement).

Also, mRNA or cDNA can be detected by traditional blotting techniques described in Sambrook et al [supra]. mRNA, or cDNA generated from mRNA using a polymerase enzyme, can be purified and separated using gel electrophoresis. The nucleic acids on the gel are then blotted onto a solid support, such as nitrocellulose. The solid support is exposed to a labelled probe and then washed to remove any unhybridized probe. Next, the duplexes containing the labeled probe are detected. Typically, the probe is labelled with a radioactive moiety.

BRIEF DESCRIPTION OF DRAWINGS

There are no drawings.

MODES FOR CARRYING OUT THE INVENTION

The following examples describe nucleic acid sequences which have been identified in N.gonorrhoeae, along with their inferred translation products.

The examples are generally in the following format:

-   -   a nucleotide sequence which has been identified in         N.gonorrhoeae. The strain used is FA1090 [Dempsey et         al. (1991) J. Bacteriol. 173:5476-5486]     -   the inferred translation product of this sequence     -   a computer analysis (e.g. PSORT output) of the translation         product, indicating antigenicity     -   homologous sequences (where relevant)     -   results of expression and purification (where relevant)

These examples typically include details of sequence homology between species and strains. Proteins that are similar in sequence are generally similar in both structure and function, and the homology often indicates a common evolutionary origin. Comparison with sequences of proteins of known function is widely used as a guide for the assignment of putative protein function to a new sequence and has proved particularly useful in whole-genome analyses.

Open reading frames (ORFs) within nucleotide sequences were predicted using the GLIMMER program [Salzberg et al. (1998) Nucleic Acids Res 26:544-8). All predicted open-reading frames longer than 60 aa were screened against the meningococcus serotype B (‘MenB’) ORFs (accession NC002183) using the BLASTP algorithm [Altschul et al. (1990) J. Mol. Biol. 215:403-410]. ORFs were considered to be gonococcus-specific if they showed sequence identity to a MenB ORF lower than 60% over the whole protein length, or matching the MenB ORF over less than 30% of the length.

Open reading frames are usually shown with a N-terminal methionine. Where this is not the case (e.g. SEQ IDs 12, 18, 20, 32, 54, 62, 66, 84, 98, 102, 104, 112, 116, 118, 126, 128, 130, 134, 136, 138, 146, 152, 162, 186, 228, 238, 240, 278, 280, 288, 290, 298, 300, 308, 314), a non-ATG start codon is present, but the N-terminus amino acid will be methionine when translated using this start codon. If an upstream start codon is used, however, the “native” amino acid will be translated (e.g. if the sequence is expressed with N-terminus fusion sequences). Even where the first amino acid is not shown as methionine, the invention encompasses sequences in which the first amino acid is methionine.

Various tests can be used to assess the in vivo immunogenicity of the proteins identified in the examples. For example, the proteins can be expressed recombinantly and used to screen patient sera by immunoblot. A positive reaction between the protein and patient serum indicates that the patient has previously mounted an immune response to the protein in question ie. the protein is an immunogen. This method can also be used to identify immunodominant proteins.

The recombinant protein can also be conveniently used to prepare antibodies e.g. in a mouse. These can be used for direct confirmation that a protein is located on the cell-surface. Labelled antibody (e.g. fluorescent labelling for FACS) can be incubated with intact bacteria and the presence of label on the bacterial surface confirms the location of the protein.

For protein expression of 14 antigens, sequences were amplified using the following primers: Restriction Sequences site NGS5 Fwd CGCGGATCCCATATG-TGGGCAGAACAACCGGC NdeI Rev CCCGCTCGAG-GTTTTCAGCAGGGGGATTG XhoI NGS7 Fwd CGCGGATCCCATATG-GCCGGTAAAGAGCAATTTAC NdeI Rev CCCGCTCGAG-AGCCAAGAAGAACCCGTTAT XhoI NGS13 Fwd CGCGGATCCGCTAGCTGCGTTGCCGACCCCG NheI Rev CCCGCTCGAG-CATGTGCCGTGCGGCGT XhoI NGS36 Fwd CGCGGATCCGCTAGC-GACACCCCGAACAATACC NheI Rev CCCGCTCGAG-AAACCTGCCCTTGATGCC XhoI NGS37 Fwd CGCGGATCCCATATG-GTAGAAGTTAAAGGCGGGG NdeI Rev CCCGCTCGAG-TTTTTTCGCGCCGCCGAA XhoI NGS38 Fwd CGCGGATCCCATATG-GCCGACGAACGCCGCC NdeI Rev CCCGCTCGAG-AAACCGATATTTAAAACCCAACAGCC XhoI NGS39 Fwd CGCGGATCCGCTAGCAACCAAGAAGGGATTACCG NheI Rev CCCGCTCGAG-TTTTTGAGCATAATGACTTTTGCCCT XhoI NGS67 Fwd CGCGGATCCCATATG-CGTGCGCACGGACACG NdeI Rev CCCGCTCGAG-GGCGGCGAGTTTTTCGC XhoI NGS106 Fwd CGCGGATCCCATATG-GCAAACAGCGGAACGATAG NdeI Rev CCCGCTCGAG-AAAATCCTGCGGGATCGGT XhoI NGS115 Fwd CGCGGATCCCATATG-GGGGGCGGCTCCGGC NdeI Rev CCCGCTCGAG-TTCGGCCAACAATGCTTCC XhoI NGSΔG115 Fwd CGCGGATCCCATATG-GATGCCCAATCTTCACAAAG NdeI Rev CCCGCTCGAG-TTCGGCCAACAATGCTTCC XhoI NGS118 Fwd CGCGGATCCCATATG-ACCGCCCTTCCCTCTGA NdeI Rev CCCGCTCGAG-CGGCTGCCATTCGCGTT XhoI NGS122 Fwd CGCGGATCCCATATG-AACCCGAACGATGCGTTTT NdeI Rev CCCGCTCGAG-AGGGTAAAACTTATTCAAATCGGCAA XhoI NGS144 Fwd CGCGGATCCCATATGGCTTCTGAAAATTCTGTAGC NdeI Rev CCCGCTCGAG-GAACACGCTTTTCATTACACCCA XhoI NGS151 Fwd CGCGGATCCCATATGCACGGTATGCATAAGAGCA NdeI Rev CCCGCTCGAG-TTGCTGATGCGGCTTTATTCG XhoI

EXAMPLE 1

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 1> which encodes amino acid sequence <SEQ ID 2; NGS1>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −5.47  Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   4.72 threshold:  0.0  PERIPHERAL Likelihood = 4.72   modified ALOM score: −1.44 Rule: cytoplasmic protein * * * Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.326(Affirmative) < succ>    bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P45941|LYQC_BACSU HYPOTHETICAL 21.5 KD PROTEIN IN CWLA-CISA INTERGENIC REGION pir||E69949 hypothetical protein yqcF-Bacillus subtilis dbj|BAA06963.1| (D32216) ORF95 [Bacillus subtilis] dbj|BAA12427.1| (P84432) YqcF [Bacillus subtilis] emb|CAB14528.1| (Z99117) yqcF [Bacillus subtilis] Length = 192 Score = 35.5 bits (81), Expect = 0.45 Identities = 36/162 (22%), Positives 77/162 (47%), Gaps 5/162 (3%) Query: 19 DSGSQYKLNIAAIPSSPNRDLKTYITLGLSKHDLHYK---SRFEILFVCSLKYDENQIFP 75 D      ++I ++   P   + +Y TLGLS H +NY+   +   I  V +++   + Sbjct: 29 DDNKSSIDILSVSDQPQEGITSYSTLGLSDHSIEGTPLRIEIV~AAMESASDIYAN 88 Query: 76 FLRWLAETIIENKKILLRGQVVYLPRSIVNS-TKMDALYVSAPFYFDDDFQVCYGEHYNI 134  L   A  II +      G +     S+ +  T M  +    PF +++D ++    + N+ Sbjct: 89 VLSTCAFNIINSNFTCAPGVIFKNVISMYDQETDMKHIMFVPPFLWEEDLELLEFSNKNV 148 Query: 135 VFPLLVPLYKQEAELVEKKGWNAFEQFLLDNEVGNLSDMNRK 176  + + +P+ + E ++ EK G + + Q LL+++  ++ D+ R+ Sbjct: 149 TWLMALPISEGELQVAEKHG-SDYLQDLLESKQIDIFDIKRE 189

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 2

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 3> which encodes amino acid sequence <SEQ ID 4; NGS2>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −7.2  Possible cleavage site: 18  >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   5.89 threshold:  0.0  PERIPHERAL Likelihood = 5.89   modified ALOM score: −1.68 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.367(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >emb|CAC01359.1|(AL390975) hypothetical protein SCP8.21 [Streptomyces coelicolor A3(2)] Length = 198 Score = 37.2. bits (85), Expect = 0.15 Identities = 29/107 (27%), Positives = 51/107 (47%), Gaps = 3/107 (2%) Query: 73 ETPEHIETLAMLASASYPDQFQLGKNIGRPWVEQSSFRHFLISLPYPYGQELEY 130 +T + +  LA+LA++          G ++++G P    + F   L++ P    ++LE Sbjct: 88 DTDKVLRPLAVLAASPQVEGVIVAPGASLDVGEPLWPGAPFTSVLVAEPGGLVEDLELDA 147 Query: 131 -MDNRFFWLLPITQTERLFLNTHSVEELETKFDEAGIDYLDINRAS 176 +D VRF  LLP+T  E  +   H    L+ ++   G D  D +R S Sbjct: 148 PLDPVFLPLLPMTPNEAAWKRVHGAPALQERWLNHGTDLRDPSRRS 194

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 3

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 5> which encodes amino acid sequence <SEQ ID 6; NGS3>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −1.69  Possible cleavage site: 32 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 33 ALOM: Finding transmembrane regions (Klein et al.)  count: 5 value:  −10.56 threshold:  0.0  INTEGRAL Likelihood = −10.56 Transmembrane 182-198  (171-201)  INTEGRAL Likelihood = −7.86 Transmembrane 251-267  (244-273)  INTEGRAL Likelihood = −7.48 Transmembrane 142-158  (136-167)  INTEGRAL Likelihood = −6.32 Transmembrane 55-71  (50-82)  INTEGRAL Likelihood = −2.97 Transmembrane 100-116  (99-117)  PERIPHERAL Likelihood = 4.72   modified ALOM score: 2.61 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----    bacterial inner membrane --- Certainty= 0.522(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P19845|NOSY_PSEST MEMBRANE PROTEIN NOSY PRECURSOR pir||S13585 nosY protein precursor-Pseudomonas stutzeri emb|CAA37717.1|(X53676) nosY [Pseudomonas stutzeri] Length = 276 Score = 163 bits (413), Expect = 2e−39 Identities = 117/275 (42%), Positives = 174/275 (62%), Gaps = 2/275 (0%) Query: 1 MNPVWIITGKEARDSLRNRWVLAAVLLLAALALSLGFLGSSPTGSVKVDPLTVTVVSLSS 60 MN VW I  KE  D LRNRW+LA  LL A LA+ + +LG++ +G +    +  T+ SL+S Sbjct: 1 MNQVWNIARKELSDGLRNRWLLAISLLFAVLAGIAWLGAAASGQLGFTSIPATIASLAS 60 Query: 61 LLSIFLIPLIAMLLSYDALIGEIERGTMALLLSYPIWRNQILAGKFVGHLIILALATTAGY 120 L+ FL+PLIA+LL+YDA++GE E GT+ LLL+YP+ R QIL GKFVGH +ILALA   G+ Sbjct: 61 LATFLMPLIALLLAYDAIVGEDEGGTLMLLLTYPLGRGQILLGKFVGHGLILALAVLIGF 120 Query: 121 GLAGITLQLANGGFDIAA-WKPFALLAASVILGAAFLSMGYLISAKVKERGTAAGISIG 179 G A + + L   G ++   +  F   + +S +LG  FL+  Y++S  KV E+ +AAG+++G Sbjct: 121 GCAALAIALLVEGVELGMLFWAFGRFHISSTLLGWVFLAFAYVLSGKNEKSSAAGLALG 180 Query: 180 VWLFFVVIFDMALLGILVADSKQVITAPVVETVLLFNPTDIYRLLNLTGYENTAMYAGMA 239 VW F  V+    +L  +  S+      ++  +LL NPTDIYRL+NL+G+E +    G+ Sbjct: 181 VW-FLFVLVFDLVLLALLVLSEGKFNPELLPWLLLLNPTDIYRLINLSGFEGSGSAMGVL 239 Query: 240 GLSGQIGLTVPVLLTAQVLWVIIPLVLAAGIFRKR 274  L   + +   VL    + W+ + L+LA  IFR+R Sbjct: 240 SLGADLPVPAAVLCLLAWIGVSLLLAYAIFRRR 274

A homolog (amino acids 226-276) was found in serogroup A N.meninigitidis but not in serogroup B, so NGS3 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 4

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 7> which encodes amino acid sequence <SEQ ID 8; NGS4>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): 1.53  Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   0.63 threshold:  0.0  PERIPHERAL Likelihood = 0.63   modified ALOM score: −0.63 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.103(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|Q59746|NOSZ_RHIME NITROUS-OXIDE REDUCTASE PRECURSOR (N(2)OR) (N2O REDUCTASE) gb|AAC44023.1|(U47133) nitrous-oxide reductase [Sinorhizobium meliloti] prf||2209347B nitrous-oxide reductase [Rhizobium meliloti] Length = 639 Score = 660 bits (1704), Expect = 0.0 Identities = 344/536 (64%), Positives = 407/536 (75%), Gaps = 23/536 (4%) Query: 1 MSDEKLEQNGLSRRSFLGTAA--ASGAGIAGAGLIGLAGCSKDGEQAAANASGAAPVAKA 58 MS+E+ +   L+RR  LGT A  A+   +   G L L+G             G A  A+A Sbjct: 1 MSNEETKMR-LNRRQMLGTTAFMAAAGAVGAGGALTLSG-------------GTATPARA 46 Query 59 QGESKPGQLSSEVGPGELDQYYGFLSGGQSGEMRLIGLPSMRELMRIPVFNMDSATGWGR 118 Q  S     S EV PGELD+YY F S GQSGE+R++G PSMRE+MRIPVFN  SATGWG+ Sbjct: 47 QETSGS---SYEVKPGELDEYYVFFSSGQSGEIRIVGAPSMREMMRIPVFNRCSATGWGQ 103 Query: 119 TNESLKVLNGNITEETRKFLKDSGLRCYPNGDLHHPHLSFTDQTYDGRYAYANDKANNRV 178 TNES KV+   +  ET +FLKD G   Y NGDLHHPH SFTD TYDGRY YANDK+N+RV Sbjct: 104 TNESRKVMTEGLLPETVEFLKDQG-GLYLNGDLHHPHPSFTDGTYDGRYLYANDKSNSRV 162 Query: 179 CRVRLDVMKADIIDIPNDSGIHGIHGLRPQRYPKTGYVFANGEHITPVSGVGK-LDDAKTWN 237 CR+RLDVMK DKII +PN   +HGLR Q+YPKTGYVF NGE   PV   GK + D  ++ Sbjct: 163 CRIRLDVMKCDKIIQLPNQHTVHGLRVQKYPKTGYVFCNGEDAVPVPNDGKTMGDKNSYQ 222 Query: 238 AVYTAIDGETMEIAWQVLVDGNLDNGDADYQGKYSFATCYNSERALTVQGASSNEQDWCV 297 A++TA+DGETME+AWQV+VDGNLDN DADYQGKY FATCYNSE   T+    ++EQDW V Sbjct: 223 AIFTAVDGETMEVAWQVMVDGNLDNVDADYQGKYCFATCYNSEEGFTLADMMASEQDWVV 282 Query: 298 VFDLKAIEEGIKAGDFKEVNGVLDGRABAKSKYTRYIPVFNSPHGCNASPDGKYIMPN 357 +F+LK IEE +  GD+KE+ GV +LDGR    S YTRY+PVPNSPHG N +PDG +++ N Sbjct: 283 IFNLKRIEEAVAKGDYKEIGGVPVLDGR--KGSPYTRYVPVPNSPHGINTAPDGIHVVAN 340 Query: 358 GKLPPTVTVLDVSKLDDLFAGKIKERDVVAEPQLGLGPLHTAFDGRGNAYTTLFIDSQM 417 GKL PTVTV DV K DDLF  KI+ RD VVAEP+LGLGPLHTA+DG+GNAYTTLFIDSQ+ Sbjct: 341 GKLSPTVTVFDVRKFDDLFDDKIQARDTVVAEPELGLGPLHTAYDGKGNAYTTLFIDSQV 400 Query: 418 VKWNIDDAIKAYGEKIDPIKQKLDVHYQPGHNHTTMGETKEADGQWLVSLNKFSKDRFL 477 KWNI+DA +AY GEK+DPI+ KLDVHYQPGHNHT+MG+TKEADG+WL+SLNKFSKDR+L Sbjct: 401 CKWNIEDAKRAYAGEKVDPIRHKLDVHYQPGHTSMGQTKEADGKWLISLNKFSKDRYL 460 Query: 478 NAGPLKPECDQLIGISGDEMRLVHDNPTFAEPHDLCLVAASKLNPGKTWDRKDPWF 533 N GPLKPE DQLI ISGDEM LVHDNPTFAEPHD  +V ASK+NP   W+R DP+F Sbjct: 461 NVGPLKPENDQLIDISGDEMVLVHDNPTFAEPHDATIVHASKINPVHVWNRDDPFF 516

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 5

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 9> which encodes amino acid sequence <SEQ ID 10; NGS5>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): 1.09  Possible cleavage site: 19 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 20 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value:   7.43 threshold:  0.0   PERIPHERAL Likelihood = 7.43  modified ALOM score: −1.99 Score for OM-PP discrimination: 4.97 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 4.97 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane? score: 0.496525 ----- Final Results -----   bacterial outer membrane --- Certainty= 0.781(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.138(Affirmative) < succ>   bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

The protein was expressed in E.coli as an insoluble 43.56 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 6

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 11> which encodes amino acid sequence <SEQ ID 12; NGS6>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −3.93  Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   6.42 threshold:  0.0  PERIPHERAL Likelihood = 6.42   modified ALOM score: −1.78 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.447(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir|F83173 outer membrane protein OprC PA3790 [imported]-Pseudomonas aeruginosa (strain PAO1) dbj|BAA05664.1|(D28119) outer membrane protein C [Pseudomonas aeruginosa] gb|AAG07177.1|AE004797_12 (AE004797) outer membrane protein OprC [Pseudomonas aeruginosa] Length = 723 Score = 77.9 bits (191), Expect = 1e−13 Identities = 58/188 (30%), Positives = 89/188 (46%), Gaps = 13/188 (6%) Query: 49 VKDLIIFDRAHGQSGTASKGGIITRNVDAILFTAQAYARYNFNPHWAAGIKAAYNYGHN 108 +TL, V+D I+F    G  G++++       NVDAR+   +  A Y    +W      AY +G N Sbjct: 546 VQDFILFSYREGMMGSSTQ-----ATNVDARIMGGELGASYQLTGNWKTDASLAYAWGKN 600 Query: 109 ETDGRPPYQIRPFEAAVQADYKNYFAHGSYNIGAATRFVAKQTRGDFDMASGLGIDKREA 168  +D R   QI P EA     Y+     G ++ G+  R VA Q R   D  + +G D  ++ Sbjct: 601 SSDDRALPQIPPLEARFGLTYE----EGDWSAGSLWRVVAPQNRIARDQGNVVGKDFDKS 656 Query: 169 AKGFTVADVYAGVNIKDKYGLRLGVNNVFNKKYVEYI--SGDHVLALSPS-VVYAPGRTY 225 A GF V  +     +     L  GV+N+F+K Y E++  +GD     S +  V  PGRT+ Sbjct: 657 A-GFGVFSLNGAYRVTRNVKLSAGVDNLFDKDYTEHLNKAGDAGFGFSANETVPEPGRTF 715 Query: 226 WLSLHAAF 233 W  +  +F Sbjct: 716 WTKVDFSF 723

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 7

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 13> which encodes amino acid sequence <SEQ ID 14; NGS7>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Hejine)  Signal Score (−7.5): 4.94  Possible cleavage site: 26 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 27 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   0.79 threshold:  0.0  PERIPHERAL Likelihood = 0.79   modified ALOM score: −0.66 Score for OM-PP discrimination: −18.85 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −18.85 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?‘0 score: 1.8846 ----- Final Results -----   bacterial periplasmic space --- Certainty= 0.929(Affirmative) < succ>   bacterial outer membrane --- Certainty= 0.211(Affimative) < succ>   bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||D72405 hypothetical protein-Thermotoga maritima (strain MSB8) gb|AAD35294.1|AE001705_5 (AE001705) hypothetical protein [Thermotoga maritima] Length = 300 Score = 81.8 bits (201), Expect = 1e−14 Identities = 72/289 (24%), Positives = 124/289 (41%), Gaps = 17/289 (5%) Query: 38 PAMPSVTIAVAALQGKLAKQADVSLKIWRSPDQLRAGVASGQFKVMMSPSNVGVNLRNQG 97 +TL, P  P++   V  + GK+    DV ++IW++P++  A + S +    + P  VG NL  +G Sbjct: 24 PLGPALIPVVPIMDGKIP--TDVKIEIWKNPEEAVAKIVSKEVDFAVLPVTVGANLYGKG 81 Query: 98 QKVGMNILTNGITQLVCKGSAIASP-QDLVGKKILVPF-KNDMPDIVLQALLKKLKIDA 155  ++ +V +    +LV    A     + L G+++  P  +    D++++  L K  + Sbjct: 82 VRIKLVGVHEWKVFYLVASDDATFDGWESLRGQEVYTPHGRGQTVDVLMRYFLSKAGLTL 141 Query: 156 HK-VSITYAATPPEAVGLFPSKGYHAVILPEPMATASLLKGKTIGINVVHGFDLVKAWGQ 214  + V I YA  P E V LF S       LPEP  +  L +GK +        D  K WG+ Sbjct: 142 DRDVKILYAP-PQEIVALFKSGKVKYAALPEPFVSMCLDRGKVV-------LDFQKEWGK 193 Query: 215 AFDTKPLIPMAGIIANEEYFHAHKAQFDIFHQDLKNALNWILANRQNAAKIGKNYLPAPE 274        IP+AG+   E      K   +   + L +++ W+  N     ++    L  P Sbjct: 194 ELGVPGRIPIAGLFVRE---GVDKETVEKVKALIDSIRWMKENLDETVQLSSEKLGIPA 250 Query: 275 PALVHGLDGAPLTVSKGSEVKNEILKFYEILMQFNPELLGGKLPDNGFF 323   L   L+          + + E+  F + L +  PE    K+PD GF+ Sbjct: 251 KILKSSLERIEFEYVPVEKCREEVETFLKKLNELYPEGF-EKIPDEGFY 298

The protein was expressed in E.coli as an insoluble 32.89 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 8

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 15> which encodes amino acid sequence <SEQ ID 16; NGS8>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): 2.39  Possible cleavage site: 15 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 16 ALOM: Finding transmembrane regions (Klein et al.)  count: 4 value:   −8.23 threshold:  0.0  INTEGRAL Likelihood = −8.23 Transmembrane 49-65  (41-73)  INTEGRAL Likelihood = −7.38 Transmembrane 83-99  (75-106)  INTEGRAL Likelihood = −7.06 Transmembrane 110-126  (100-133)  INTEGRAL Likelihood = −4.41 Tranamembrane 164-180  (163-187)  PERIPHERAL Likelihood = 5.89   modified ALOM score: 2.15 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----    bacterial inner membrane --- Certainty= 0.429(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P38044|NRTB_SYNP7 NITRATE TRANSPORT PERMEASE PROTEIN NRTB pir||S30892 nitrate transport protein nrtB-Synechococcus sp. (strain PCC 7942) emb|CAA43810.1|(X61625) nitrate transporter [Synechococcus sp.] prf||1908370A nitrate transporter [Synechococcus sp.] Length = 279 Score = 67.5 bits (164), Expect = 1e−10 Identities = 54/202 (26%), Positives = 96/202 (46%), Gaps = 7/202 (3%) Query: 4 VALWAWGSAVFGEFMLPAPVEFQKSL--DLLKHFQEN-----EIGISLWRSVVGISVAL 56 +A+W  SA+ G+  LP P+ V   +    +++ F +N      +G+ +  S+  +++ Sbjct: 36 LAIWQVISAILGQDRLPGPINVVANTWMPYIVEPFFDNGGTSKGLGLQILISLQRVAIGY 95 Query: 57 IAGLAAGLVAGLVAGSFKTAMALLKPVITILLAMPPIIWVVMALFWFGFGNPSVLFTIIV 116 +     G++ G V G  K     L PVI +L  +PP+ W  ++L  F   N S +F I + Sbjct: 96 LLAACTGILVGGVLGMSKFLGKGLDPVIQVLRTVPPLAWFPISLMVFQDANTSAIFVIFI 155 Query: 117 LVAPLTFASAAVGMASVNKQHEELFDAYKLGRLKKIRYLYIPHLTGYVISSVGVAVAMGV 176         + AVG+  +   +  +    KL +   I  + IP    YV + + +AV + Sbjct: 156 TAIWPIIINTAVGINQIPDDYNNVARVLKLSKKDYILNILIPSTVPYVFAGLRIAVGLAW 215 Query: 177 KAVIMAELLGASKGVGARIADA 198  A++ AE+L A  G+G  I DA Sbjct: 216 LAIVAAEMLKADGGIGYFIWDA 237

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 9

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 17> which encodes amino acid sequence <SEQ ID 18; NGS9>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −5.07  Possible cleavage site: 29 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 1 value:   −1.81 threshold:  0.0  INTEGRAL Likelihood = −1.81 Transmembrane 97-113  (96-113)  PERIPHERAL Likelihood = 4.24   modified ALOM score: 0.86 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----    bacterial inner membrane --- Certainty= 0.172(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P97027|SSUB_BACSU PUTATIVE ALIPHATIC SULFONATES THANSPORT ATP-BINDING PROTEIN SSUB pir||G69816 nitrate ABC transporter (binding protein) homolog ygaL- B. subtilis emb|CAB07520.1|(Z93102) hypothetical 30.6 kd protein [Bacillus subtilis] emb|CAB12711.1|(Z99108) similar to nitrate ABC transporter (binding protein) [Bacillus subtilis] Length = 274 Score = 99.5 bits (247), Expect = 3e−20 Identities = 68/181 (37%), Positives 102/181 (55%), Gaps = 9/181 (4%) Query: 4 LFGPSGCGKTTVLRLIAGLETPKSGTIRNTFH-------KTGFLFQENRLPENLTAMQNI 56 L GPSGCGK+T+L++IAGL++   G++            + GF+FQE+RL   LT  QNI Sbjct: 56 LIGPSGCGKSTLLKIIAGLDSEYDGSVEINGRSVTAPGIQQGFIFQEHRLFPWLTVEQNI 115 Query: 57 A--IFMDNPDEGEIVALAAKVGLTAGDLNKYPTELSGGMAKRVAFLRLLLCGCDLALLDE 114 A  + + +P   + V    ++    G    YP ELSGGM++RVA  R LL   ++ LLDE Sbjct: 116 AADLNLKDPKVKQKVDELIEIVRLKGSEKAYPRELSGGMSQRVAITRALLREPELLLDE 175 Query: 115 PFVGLDRDLRDILVAMLVEKIERQGMACILVTHDRFEAARLSHEIMLLSAKGMNVQNVIT 174 PF  LD   R  L  +L++   ++    ILVTHD  E+  L +E+ +L AK   +  ++ Sbjct: 176 PFGALDAFTRKHLQDVLLDIWRKKTTNILVTHDIDESVYLGNELAILKAKPGKIHKLMP 235 Query: 175 L 175 + Sbjct: 236 I 236

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 10

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 19> which encodes amino acid sequence <SEQ ID 20; NGS10>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal score (−7.5): 2.27  Possible cleavage site: 26 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   5.14 threshold:  0.0  PERIPHERAL Likelihood = 5.14   modified ALOM score: −1.53 *** Reasoning Step: 2 imb2 HYPID: 2 CFP: 0.1 ----- Final Results -----    bacterial inner membrane --- Certainty= 0.100(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>     bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||A82615 surface protein XF1981 [imported]-Xylella fastidiosa (strain 9a5c) gb|AAF84783.1|AE004017_6 (AE004017) surface protein [Xylella fastidiosa] Length = 1190 Score = 50.2 bits (119), Expect = 2e−05 Identities = 59/210 (28%), Positives = 92/210 (43%), Gaps = 5/210 (2%) Query: 17 SIGTSAEANAPGAALGGSSEASKFSIAEGYLASSDGYGAIAIGSAAKI-KQLEKGTIN 75 ++G    A+A GA A+G  + AS K S A G  A +   G++A+G  AK   +  + Sbjct: 876 AVGVGTLASAEGATAVGSGAAASGKGSTAIGRNAVASADGSVALGDGARGAESYTG 935 Query: 76 HIVGNDNKGLYVDADGNVTKITVRTESEKDILSRYGQTYGAVALGFRSSSHNLFA----S 131    G  N  +   + G+ +K   RT S                L   +   N + Sbjct: 936 KYSGLQNNTVGTVSVGDASKGETRTVSNVADAKEATDAVNLRQLDRVAQDANRYVDNKIE 995 Query: 132 SFGAFSTATAIESLAVGDSSQSTGYRSATFGSHSRALAEESLALGYETRANYGSVALGA 191 S     T   + SL    +  + G  +   G  + A   +S+A+G +  A+A  +VA+G Sbjct: 996 SLSEGQTFVKVNSLNNSATPIAAGVDATAIGVGATASGADSIAMGNKASADNAVAIGN 1055 Query: 192 ESVANEENTVSVSSDTLKRKIVNVIADGTED 221  SVA+  NTVSV S   +R++ NVA GT D Sbjct: 1056 HSVADRANTVSVGSAGSERQVTNVAAGTAD 1085 >sp|P10858|YADA_YERPS INVASIN PRECURSOR (OUTER MEMBRANE ADHESIN) pir||S04534 invasin precursor-Yersinia pseudotuberculosis plasmid pIBI emb|CAA32088.1|(X13883) Yop1 preprotein (AA 1-434) [Yersinia pseudotuberculosis] prf||1411295A invasin [Yersinia pseudotuberculosis[ Length = 434 Score = 42.1 bits (98), Expect = 0.006 Identities = 35/134 (26%), Positives = 68/134 (50%), Gaps = 28/134 (20%) Query: 116 AVALGFRSSSHLFASSFGFSTATAIESDSSQSTGYRSATFGSHSRA-------- 167 ++A+G  + +    A + G+ S AT + S+A+G  S++ G  + T+G+ S A Sbjct: 107 SIAIGATAEAAKPAAVAVGSGSIATGVNSVAIGPLSKALGDSAVTYGASSTAQKDGVAIG 166 Query: 168 ----LAEESLALGYETRANAYGSVALGA----------------ESVANEENTVSVSSDT 207      ++  +A+G+ ++ +A  SVA+G                  S  + EN+VS+  ++ Sbjct: 167 ASDTGVAVGFNSKDAQNSVAIGHSSHVAADHGYSIAIGDHSKTDRENSVSIGHES 226 Query: 208 LKRKIVNVADGTED 221 L R++ ++A GTED Sbjct: 227 LNRQLTHLAAGTED 240

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 11

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 21> which encodes amino acid sequence <SEQ ID 22; NGS11>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −0.16  Possible cleavage site: 60 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value:   4.67 threshold:  0.0   PERIPHERAL Likelihood = 4.67   modified ALOM score: −1.43 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.297(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P10858|YADA_YERPS INVASIN PRECURSOR (OUTER MEMBRANE ADHESIN) pir||S04534 invasin precursor-Yersinia pseudotuberculosis plasmid pIBI emb|CAA32088.1|(X13883) Yop1 preprotein (AA 1-434) [Yersinia pseudotuberculosis] prf||1411295A invasin [Yersinia pseudotuberculosis] Length = 434 Score = 41.3 bits (96), Expect = 0.007 Identities = 27/71 (38%), Positives = 48/71 (67%), Gaps = 4/71 (5%) Query: 16 QLNRLSKRTNRVGASAAALASL-KPAQLGKNDKFAFSLGFGSYKNAQAVAMGAVFKPAEN 74 +L++L KR ++  AS+AAL SL +P  +GK +   F+ G G Y+++QA+A+G+ ++  E+ Sbjct: 353 RLDKLDKRVDKGLASSAALNSLFQPYGVGKVN---FTAGVGGYRSSQALAIGSGYRVNES 409 Query: 75 VLLNVAGSFAG 85 V L    ++AG Sbjct: 410 VALKAGVAYAG 420

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 12

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 23> which encodes amino acid sequence <SEQ ID 24; NGS12>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −1.29  Possible cleavage site: 61 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 62 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   6.36 threshold:  0.0  PERIPHERAL Likelihood = 6.36   modified ALOM score: −1.77 Score for OM-PP discrimination: 6.03 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 6.03 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane? score: 0.602784 ----- Final Results -----    bacterial outer membrane --- Certainty= 0.867(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.158(Affirmative) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>     bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 13

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 25> which encodes amino acid sequence <SEQ ID 26; NGS13>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −3.64  Possible cleavage site: 51 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:  calculated from 21 ALOM: Finding transmembrane regions (Klein et al.)  count: 1 value:   −1.01 threshold:  0.0  INTEGRAL Likelihood = −1.01 Transmembrane 36-52  (36-52)  PERIPHERAL Likelihood = 5.14   modified ALOM score: 0.70 Rule: inner or outer membrane protein Rule: inner or outer membrane protein Rule: cytoplasmic membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----    bacterial outer membrane --- Certainty= 0.790(Affirmative) < succ>    bacterial inner membrane --- Certainty= 0.742(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gb|AAC33455.1|(AF067083) outer membrane protein homolog [Vitreoscilla sp.] Length = 217 Score = 236 bits (602), Expect = 2e−61 Identities = 134/217 (61%), Positives = 166/217 (75%) Query: 1 MTFFKPSTVVLTASALALSGCVADPVTGQQSPNKSAMYGLGGAAVCGWGALTHSGKGAR 60 M  +K  +++ T +A+ALS C  DP+TGQ   N + +  LGGAA CGIVGALTH  KGAR Sbjct: 1 WKAWKKFSLMATVAAVALSACATDPMTGQVDRNNTVLGALGGAATCGIGALTHGSKGAR 60 Query: 61 NSALACGAIGAGVGGYMDYQEQRLRQNLAGTQIEIQRQGNQIRLVMPESVTFATGSAALG 120 NSALACGAIGAGVG YMD+QE++LRQ+LA TQ+E+ R G++IRLVMPES+TFATGS  L Sbjct: 61 NSALACGAIGAGVGAYMDHQERQLRQSLANTQVEVNRVGDEILVMPESITFATGSYQLN 120 Query: 121 GSAQYALNTAAQTLVQYPDTTLTINGHTDNTGSDAVNNPLSQHRAQAVAYYLQTRGVAAS 180 SA  +LN+ +  L QY DTT+ I GHTD+TGSDA+N PLS++RA AVA YL +R VA++ Sbjct: 121 SSASTSLNSVSSVLAQYTDTTINIVGHTDSTGSDAINEPLSRNRASAVANYLVSRNVASN 180 Query: 181 RLTVYGYGSHMPVASNATVEGRAQNRRVEILINPDQR 217 R+T  G G   PVASN TV GRA+NRRVEI +NP QR Sbjct: 181 RITTVGAGCRQPVASNNTVAGRAENRRVEITVNPIQR 217 >gb|AAD40344.1|U88088_22 (U88088) OmpA [Pseudomonas alcaligenes] Length = 220 Score = 130 bits (328), Expect = 1e−29 Identities = 90/219 (41%), Positives = 127/219 (57%), Gaps = 6/219 (2%) Query 7 STVVLTASALALSGCVA---DPVTGQQSPNKSAMYGLGGAAVCGIVGALTHSGKGARNSA 63 S +  +     L+GC +   +  T + +    A   L GA    ++G   +  +GA   A Sbjct: 3 SVIAASLVIFTLTGCASIQNEDGTTKNTALYGAGGALAGAVAGALIGK-ENRAQGALIGA 61 Query: 64 LACGAIGAGVGGYMDYQEQRLRQNLAGTQIEIQRQGNQIRLVMPESVTFATGSALLLGGSA 123    G++GAG G Y D QE  LR+ + G+ ++++RQG++I +VMP ++TFATG A +  + Sbjct: 62 AVAGSLGAGYGYYADKQEAELREQMKGSGVQVERQGDEIVIVMPGAITFATGKAEIQPNF 121 Query: 124 QYALNTAAQTLVQYPDTTLTINGHTDNTGSDAVNNPLSQHRAQAVAYYLQTRGVAASRLT 183    LN  A +   YPD+ L + GHTD+ GS   N  LSQ RAQ+VA +L+  GV   R+ Sbjct: 122 ANTLNQLAGSFPNYPDSRLIVTGHTDSVGSYEANELLSQRRAQSVAQFLRGNGVQTDRIE 181 Query: 184 VGYGHMPVASNATEGRAQNRRVEILINPDQRAVNAA 222 V G G + PVASNAT EGRAQNRRVEI + P  RAV  A Sbjct: 182 VIGAGPNQPVASNATAEGRAQNRRVEIKLAP--RAVQQA 218

The protein was expressed in E.coli as a soluble 22.55 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 14

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 27> which encodes amino acid sequence <SEQ ID 28; NOS14>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −5.32  Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   3.39 threshold:  0.0  PERIPHERAL Likelihood = 3.39   modified ALOM score: −1.18 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.254(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 15

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 29> which encodes amino acid sequence <SEQ ID 30; NGS15>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −1.75  Possible cleavage site: 45 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   5.89 threshold:  0.0  PERIPHERAL Likelihood = 5.89   modified ALOM score: −1.68 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.232(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P10487|RCI1_ECOLI SHUFFLON-SPECIFIC DNA RECOMBINASE pir||S03815 probable integrase-Escherichia coli dbj|BAA77989.1|(AB027308) shufflon-specific DNA recoinbinase [Plasmid R64] Length = 384 Score = 67.1 bits (163), Expect = 3e−10 Identities = 75/301 (24%), Positives = 125/301 (40%), Gaps = 34/301 (11%) Query: 68 KVKMMTLSEAMRKYLNETLGAGRSKKMGL---RFLMEFPIGGIGIDKLKRSDFAEHVMQR 124 +++ M+LS A+ KYL       +  +        +  PI    +D++   D A +   R Sbjct: 5 RIRKMSLSRALDKYLKTVSVHKKGHQQEFYRSNVIKRYPIALRNMDEITTVDIATYRDVR 64 Query: 125 RRGIPELDIAPIAASTALQELQYIRSVLKHAFYVWGLEIGWQELDFAANGLKRSNMVAKS 184    I      PI  +T   EL  + S+   A   WG            N ++       S Sbjct: 65 LAEINPRTGKPITGNTELELALLSSLFNIARVEWG--------TCRTNPVELVEKPKVS 116 Query: 185 AIRDRLPTTEELQTLTTYFLRQWQSRKSSIPMHLIMWLAIYTSRRQDEICRLLFDDWHKN 244 + RDR  T+E + L+YF      R+ ++ +++I  LA+ T+ RQ EI  L    W Sbjct: 117 SGRDRRLTSSEBRRLSRYF------REKNLMLYVIFHLALETAMRQGEILAL---RWEHI 167 Query: 245 DCTRPVRDLKNPNGSTGNNKEFDILPMALPVIDELPEESVRKRMLANKGIADSLVPCNGK 304 D    V  L  P    G++++  +   A   +  +P             +  ++ Sbjct: 168 DLRHGVAL--PETNGHSRDVPLSRRARNFLQMMP-----------VNLHGNVFDYTAS 214 Query: 305 SVSAAWTRACKTLGIKDLRFHULREEAATRMAEDG-FTIPQNQRVTLHDGWNSLQRYVSVR 364     AW  A + L I+DL FHDLRHEA +R  E G   + ++  ++ H   N L+RY  +R Sbjct: 215 GFKNAWRIATQRLRIEDLHRHDLRHEAISRFFELGSLNVMEIAAISGHRSMNMLKRYTHLR 275

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 16

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 31> which encodes amino acid sequence <SEQ ID 32; NGS16>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −3.64  Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   4.67 threshold:  0.0  PERIPHERAL Likelihood = 4.67   modified ALOM score: −1.43 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.262(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P10484|T1M1_ECOLI TYPE I RESTRICTION ENZYME ECOR124II M PROTEIN (M.ECOR124II) pir||S02166 type I site-specific deoxyribonuclease (EC 3.1.21.3) EcoR124/3 chain hsdM-Escherichia coli plasmid R124/3 emb|CAA31541.1|(X13145) hsdM protein (AA 1-520) [Escherichia coli] Length = 520 Score = 44.4 bits (104), Expect = 0.002 Identities = 65/235 (27%), Positives = 99/235 (41%), Gaps = 55/235 (23%) Query: 107 NRKKAGGYAEYITGGSLRRLVAARRYCGEHPGVFDGAAGSG--------QLEQYIEPS 158 N  K+GG  E+ T   + +L+A            ++D AAGSG        Q + +I Sbjct: 191 NAGKSGG--EFFTPQHVSKLIAQLAMHGQTHVNKIYDPAAGSGSLLLQAKKQFDNHIIEE 248 Query: 159 DFRAVEIQAEACRALLQNYPAAKVYNTSLFL--------------------YTDGEPQDC 198  F   EI          N+    +   ++FL                     + D +P D Sbjct: 249 GFFGQEI----------NHTTYNLARMNMFLHNINYDKRDIKLGNTLTEPHFRDEKPFDA 298 Query: 199 TVMNPPFSIKLKDLSEDEKSRIAQEYPWKKSGV------ADEIFVLKGLE--NARRFGFF 250  V NPP+S+K   +  D+ + I  E  +  +GV      AD  FVL  L   +A+ Sbjct: 299 IVSNPPYSVKW--IGSDDPTLINDER-FAPAGVLAPKSKADFAFVLHALNYLSAKGRAAI 355 Query: 251 ILFPGIAYR-KSEQRFRE-IIGNRLAE--LNRIQNAFEDTPIEVLLLVIDKDKTD 301 + FPGI YR  +EQ+ R+ ++ N   E  ++   N F  T I V +LV+ K KTD Sbjct: 356 VCFPGIFYRGGAEQKIRQYLVDNNYVETVISLAPNLFFGTTIAVNILVLSKHKTD 410

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 17

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 33> which encodes amino acid sequence <SEQ ID 34; NGS17>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −5.29  Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   2.60 threshold:  0.0  PERIPHERAL Likelihood = 2.60   modified ALOM score: −1.02 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.284(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_052389.1|translocator YopD [Yersinia enterocolitica] sp|P37132|YOPD_YEREN YOPD PROTEIN gb|AAD16812.1|(AF102990) translocator YopD [Yersinia enterocolitica] Length = 306 Score = 32.1 bits (72), Expect = 8.2 Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 17/93 (18%) Query: 13 MLAAKRAAKESTRQERAVKRAGTVRNVDRNRLSARSKAQKENIARMLSGAKVSEDEALTC 72 +L   R A+E   Q+R ++   T+             AQKE +A M+SGAK+    A+ Sbjct: 89 LLELARKAREMGLQQRDIENKATI------------SAQKEQVAEMVSGAKLMIANAVVS 136 Query: 73 GIMMRLSLQDMRYACNQELINFAEHIVKQVQRL 105 GIM   S     ++  +E+      IVKQ Q L Sbjct: 137 GIMAATSTVASAFSIAKEV-----KIVKQEQIL 164

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 18

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 35> which encodes amino acid sequence <SEQ ID 36; NGS18>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −2.56  Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   4.56 threshold:  0.0  PERIPHERAL Likelihood = 4.56   modified ALOM score: −1.41 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.397(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 19

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 37> which encodes amino acid sequence <SEQ ID 38; NGS19>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −4.12  Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   8.49 threshold:  0.0  PERIPHERAL Likelihood = 8.49  modified ALOM score: −2.20 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.250(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_043483.1|orf14 [Bacteriophage HP1] sp|P51716|YO14_BPHP1 HYPOTHETICAL 14.9 KD PROTEIN IN REP-HOL INTERGENIC REGION (ORF14) pir||S69520 hypothetical protein 14-phage HP1 gb|AAB09199.1|(U24159) orf14 [Bacteriophage HP1] Length = 133 Score = 73.3 bits (179), Expect = 1e−12 Identities = 44/129 (34%), Positives = 74/129 (57%), Gaps = 6/129 (4%) Query: 1 MFIPAALHKDEHSAYGVTIPDLPGCFSCGDTVEEAVANARSAAYMHIDGMIEDGGFKNLA 60 M  P  + K  +  Y V++PD+PGCFS GDT+ EA+ NA+ A   HI+GM+ED   + L Sbjct: 1 NLYPICIEK-VNDGYVVSVPDVPGCFSAGDTLSEAMLNAKEAISFHIEGMLEDD--EELP 57 Query: 61 VSS-IADLSQEPDYHGATWVMIEIDPAKISRQQIRFNVSWPQYLLDRVDEY--TSANHET 117  S+ I     +P+Y      ++++D   +  +  + N++ P  LL R+D++  T   ++ Sbjct: 58 KSNPIEQYINQPEYKDFIVTVVDVDLTHLMGKAEKINITVPALLLHRIDQFIATHPEYKN 117 Query: 118 RSGFLAKAA 126 RS FL++ A Sbjct: 118 RSNFLSQLA 126

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 20

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 39> which encodes amino acid sequence <SEQ ID 40; NGS20>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −0.1  Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   7.58 threshold:  0.0  PERIPHERAL Likelihood = 7.58   modified ALOM score: −2.02 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.057(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 21

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 41> which encodes amino acid sequence <SEQ ID 42; NGS21>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −3.52  Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   5.83 threshold:  0.0  PERIPHERAL Likelihood = 5.83   modified ALOM score: −1.67 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.311(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_040628.1|cI (repressor; 237) [bacteriophage lambda] ref|NP_061378.1|phage lambda repressor protein CI [Escherichia coil] sp|P03034|RPC1_LAMBD REPRESSOR PROTEIN CI pir||RPBPL repressor protein cI-phage lambda emb|CAA24991.1|(X00166) coding sequence cI gene [bacteriophage lambda] gb|AAA96581.1|(J02459) cI (repressor; 237) [bacteriophage lambda] emb|CAB96428.1|(AJ277653) phage lambda repressor protein CI [Escherichia coli] Length = 237 Score = 62.5 bits (151), Expect = 5e−09 Identities = 36/85 (42%), Positives = 51/85 (59%) Query: 2 KKRELNEIETAECAELKRIFNSKKEELKLTQYKLAEAVGVTQSAVNHYLNGTNALNASIA 61 KK+ L + + +  LK I+  KK EL L+Q  +A+ +G+ QS V    NG NALNA  A Sbjct: 4 KKKPLTQEQLEDARRKKAIYEKKKELGLSQESVADKMGMGQSGVGALFNGINALNAYNA 63 Query: 62 SQFAKILQIPVSDFSLRLAEEISSM 86 +  AKIL++ V +FS  +A EI  M Sbjct: 64 ALLAKILKVSVEEFSPSIAREIYEM 88

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 22

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 43> which encodes amino acid sequence <SEQ ID 44; NGS22>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −2.6  Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   7.74 threshold:  0.0  PERIPHERAL Likelihood = 7.74   modified ALOM score: −2.05 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.072(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||S30432 hypothetical protein-Streptomyces clavuligerus plasmid pSCL Length = 307 Score = 43.6 bits (102), Expect = 0.002 Identities = 25/86 (29%), Positives = 49/86 (56%), Gaps = 2/86 (2%) Query: 6 MGMAFKT-GIPRGRFVLVLCDCANDDGLCYPSQETLAEDTGFAETAVRQHIKWLKDNN 64 MGM F   G+   ++ +L+   +  +  G C+PS++ L +D G + + V++  +L   N Sbjct: 1 MGMVFAAEGLDGSEKLLLLGYTNWTDPYGYCWPSEDRLVDDCGTSRSTVQRTKRKLVKKN 60 Query: 65 FIKSARRQRGR-ERKSDIYRINVALL 89  ++S RR+  + E  S++ R+N+ LL Sbjct: 61 LLRSVRRKNSKGEPISNLSRVNLPLL 86

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 23

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 45> which encodes amino acid sequence <SEQ ID 46; NGS23>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −2.8  Possible cleavage site: 59 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   0.05 threshold:  0.0  PERIPHERAL Likelihood = 0.05   modified ALOM score: −0.51 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Result -----     bacterial cytoplasm --- Certainty= 0.195(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >sp|P07905|DNAC_ECOLI DNA REPLICATION PROTEIN DNAC pir||XMECNC DNA replication protein dnaC-Escherichia coli (strain K-12) Length = 245 Score = 110 bits (275), Expect = 2e−23 Identities = 75/224 (33%), Positives = 116/224 (51%), Gaps = 23/224 (10%) Query: 50 EAADEMAAYAETLRRGAMRDA----------LEKRIGRSGIAPRFRNCRIENYAV--SDS 97 +  +E+ A+ +   +GA+R A          +++   RSGI P  +NC  ENY V Sbjct: 24 KTGEELLAWQK--EQGAIRSAALERENRAMKMQRTFNRSGIRPLHQNCSFENYRVECEGQ 81 Query: 98 IPGMARAKAAAAEYAANFADVLQTGRSMIFSGRRGTGKNHLACGIAREVIAAGKSALVIT 157 +  +++A+    E+  N A       S IFSG+ GTGKNHLA  I  E++  GKS L+IT Sbjct: 82 MNALSKARQYVEEFDGNIA-------SFIFSGKPGTGKNHLAAAICNELLLRGKSVLIIT 134 Query: 158 VGDMLRTVKDSF--GGGGEAGAVGIFVKPDLLVLDEFGAGSLSETDGRILFSVVNARYER 215 V D++  +KD+F   G  E   +      DLLV+DE G  + S+ +  I+  +V+ R Sbjct: 135 VADIMSAMKDTFRNSGTSEEQLLNDLSNVDLLVIDEIGVQTESKYEKVIINQIVDRRSSS 194 Query: 216 LMPMLVLTNLTAEAFRENTDARIRDRLRDGGGKLIPFDWESTRA 259   P  +LTN   E   +    R+ DR+R G    + F+W+SYR+ Sbjct: 195 KRPTGHLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWDSYRS 238

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 24

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 47> which encodes amino acid sequence <SEQ ID 48; NGS24>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)  Signal Score (−7.5): −5.76  Possible cleavage site: 26 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)  count: 0 value:   1.43 threshold:  0.0  PERIPHERAL Likelihood = 1.43   modified ALOM score: −0.79 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.112(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_053228.1|pXO2-73 [Bacillus anthracis] gb|AAF13678.1|AF188935_76 (AF188935) pXO2-73 [Bacillus anthracis] Length = 541 Score = 125 bits (315), Expect = 9e−28 Identities = 139/535 (25%), Positives = 254/535 (46%), Gaps = 70/535 (13%) Query: 14 PVLFIGTGMSLRYLDNSYTWDGLLSKIAIDLFGDDREYLNIKSRYCEDGRFQYEEIAEEL 73 P LFIG+G S RYL N   W GL+ K + +L   + EY      Y       + E+AE + Sbjct: 19 PFLFIGSGFSKRYL-NLEDWAGMKKFS-NLMPYEFEY------YSSTANKDWAEVAELM 70 Query: 74 QSKFDKVL--ENDPDGEFKEINDKFFENMRAGNTLSRFKIYISTLLSQLNYK----DNSN 127    F  +   E   +   KE  D      R  +  S  K+ ++  L+ + YK    + ++ Sbjct: 71 AKDFHPIWWKEQQFENNRKEFKD------RISSKQSPLKVEVAKYIiNSIEYKYGLDEKND 124 Query: 128 TELSELKKARKNVGSIITTNYDKLAQDIFEFNPL---IGN-DILLSNPY--GSVYKIHGC 181  E°+ LKK    +  IITTN+D L + IFE   +   IG   ++L S+P     +YKIHGC Sbjct: 125 KEIAALKKIV--IDGIITTNWDLLLEQIFEEQEMQVYIGQKELLFSHPLEINEIYKIHGC 182 Query: 182 VDDPSKIIITKKDYEKFKEKYELIRAQLLSLFIHNPIIFLGYNVGDENIKEILKTIFTYV 241    P  +++T  DY+ + EK   + A+LL++FI +P+IFLGY++ D+NI++ILK I   + Sbjct: 183 SSIPDSLVLTTSDYKGYNEKNAYLAAKLLTVFIEHPVIFLGYSISDDNIQQIILKAITRCL 242 Query: 242 EQNSPSANKIRRNFLLVEYEPESNNEDIVEDIDIT-GFSTIRINKIKTDNFSQIYKALA 300 +Q++    K R    L+  E     ED  E++  +T G  T+ I ++KT+++ +IY ALA Sbjct: 243 DQDNIHKLKDR----LIFVERAGQEEDSFENNSSLTIGKITVPITRVKTNDYEKIYNALA 298 Query: 301 ELTLPISAMDVRKFQSIAKEIYTGGNIKVSF---TEDMDNLNNSDKVVAIGSTKTISYNF 357 +     S   +R+ +S   E+    + +        + D+  + + V+ +G  K + Sbjct: 299 QNKRKFSMKMMRQMKSQIYELVKTNDPEEKIYVVDGEYDDTQDIEFVIGLG-VKNVVEEM 357 Query: 358 QTTSEMMSN----------------YFKIIEEENS----QLLKLIDKHSIASTQYFPI-- 395 Q+  E+ ++                + +++ +E       ++K+     + S QY P+ Sbjct: 358 QSNHEISADKELSEHGYGGISDIELFNELLSDEPKYDYDSIVKISLPQILRSNQYVPLFR 417 Query: 396 YGFSRICSDIHKEAVLKRQQKEKLDHFIEEINRRCKNNHSSIQSILDDENISDTYKNDAI 455 Y       D   ++ +K + K +   F+ E  ++   N S      + + +   + +  + Sbjct: 418 YVLESSVEDELLDSKIKNKLKMRYTDFIITETQKNIKLDWQFKNLDEVLKGFPDIKV 477 Query: 456 AWG----IWNNQLSEDEVENYL---KNFVNKKN----THYKRLLCMFDYKKYADT 499 A      +    L+ D+++++L     FV +KN    T  +RL  ++D+ KY  + Sbjct: 478 AIEQIPLLGQKNLNNCDDLDFLIKNSKFVKEKNTPERTGIRRLFRIYDWLKYGQS 532

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 25

A DNA sequence was identified in N,gonorrhoeae <SEQ ED 49> which encodes amino acid sequence <SEQ ID 50; NGS25>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 4.76837e−07    Possible cleavage site: 56 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:  calculated from 21 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  6.68 threshold:  0.0    PERIPHERAL Likelihood =  6.68   modified ALOM score:  −1.84 Rule: inner or outer membrane protein Rule: inner or outer membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----      bacterial outer membrane --- Certainty= 0.790(Affirmative)      < succ>      bacterial inner membrane --- Certainty= 0.700(Affirmative)      < succ>     bacterial periplasmic space --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear)       < succ>

The protein has homology with the following sequences in the databases: >gi|7433O05|pir||B70313 cytochrome-C peroxidase (EC 1.11.1.5)- Aquifex aeolicus gi|2982865|gb|AAC06485.1|(AE000675) cytochrome C peroxidase [Aquifex aeolicus] Length = 355 Score = 345 bits (885), Expect = 7e−94 Identities = 180/336 (53%), Positives = 237/336 (69%), Gaps = 12/336 (3%) Query: 59 EDQDLLKRAQGVFQPLPTVEEMQKIRPFTEEQVKLGHQLWYEPRLSKGNTVSCNSCHNLA 118 +D++LLK A+  F+PLP V E  +  P T E+VKLG  L+Y+PRLSK   +SCN+CHNLA Sbjct: 22 DDKELLKKMARQYFKPLPKVAENPQ-NPVTPEKVKLGKMLYYDPRLSKSGLISHCNTCHNLA 80 Query: 119 SAGVDNMPTSQGHKGQFGGRNSPTALNAALLGSQFWDGRAADVEEQAGGPLVNPVEMAND 178   GVDN+PTS GH+   G RN+PT  NAA+  +QFWDGRA DVEEQA GP+VNP+EMAN Sbjct: 81 RYGVDNLPTSIGHRWAIGPRNAPTVYNAAIHIAQFWDGRAKDVEEQALGPIVNPIEMAN- 139 Query: 179 SQEAAAAKIAKVPEYQEFKAFP-EDGAVSFKNITTALGAFERTLLTPTKWDEYLKGNV 237 ++E A   +  +PEY E+FKKAFP E   V ++NI  A+GAFERTL+TP+++DE+LKGN Sbjct: 140 TEENAVKTLKSIPEYVELFKKAFPNEKDPVKYENIGKAIGAFERTLMTPSRFDEFLKGNT 199 Query: 238 NALSEQERKGRAFDNGCIACHNGNLGGTTFQKRGLVQGPYWK------FIEDP--KR 289  AL+EQE++G++ F++ GC+ACHNG  +GG  F KFG++   YWK       +  P  K Sbjct: 200 KALTEQEKRGLKTFIEVGCVACHNGPGVGGNMFAKFGMIT-EYWKVTYPYVLVGKPAIKV 258 Query: 290 DKGEADVTKKTEDEFFFRVPGLRNVAKTYPFHNGSVWELDKAVTIMGKAQLGKDIPKED 349 D GR  VTKK ED F F+VP LRN+  TYPYFH+GSVW L+ AV IM K QLGK++  + Sbjct: 259 DFGRFGVTKKEEDMFVFKVPSLRNIEHTYPYFHDGSVWSLEDAVRIMAKTQLGKELTDQQ 318 Query: 350 VDNIVVFLNALSGNVSESARTHPELPLTAPMESKPD 385 V +IV FL AL+G + + A  +PELP +     KP+ Sbjct: 319 VKDIVAFLKALTGKIPKHALEVPELPPSTDKTPKPE 354

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 26

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 51> which encodes amino acid sequence <SEQ ID 52; NGS26>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.610001    Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  5.04 threshold:  0.0    PERIPHERAL Likelihood =  5.04   modified ALOM score:  −1.51 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.127(Affirmative)       < succ>     bacterial periplasmic space --- Certainty= 0.000(Not Clear)     < succ>      bacterial outer membrane --- Certainty= 0.000(Not Clear)      < succ>      bacterial inner membrane --- Certainty= 0.000(Not Clear)      < succ>

The protein has homology with the following sequences in the databases: >pir||T13296 hypothetical protein 8-Streptococcus phage phi-O1205 gb|AAC79524.1|(U88974) ORF8 [Streptococcus thermophilus temperate bacteriophage O1205] Length = 157 Score = 62.5 bits (151), Expect = 2e−09 Identities = 53/161 (32%), Positives = 86/161 (52%), Gaps = 8/161 (4%) Query: 5 TLYRCDVQAALDYYFDSETEREDTLEAV--IGQFEVKAQSVIAYIKNQEITEKMLEGH 62 TLY     +    +   D ET + DTLEA+     +E K +  +  IK+ E   +  + Sbjct: 3 TLYELTDQLLEIYNMDVDDET-KLDTLEAIDWTTDYENKVEGYVKVIKSLEADIEARKNE 6 Query: 63 IRQMTGKLKAAKARNQSLKDYLARNMQAAGITEIKADDGTFKASFRKSEAVVILDEAQIP 122  +++ G  K+ +++   LK  LA +M   G T +  D   FK  FRKSEAVV+ +E ++P Sbjct: 62 KKRLDGLNKSDQSKIDKLKTALAVSMAETGQTRV--DTTLFKVGFRKSEAVVV-NEEKLP 118 Query: 123 AEFMREAVKTEPDKTAIRXAIESGRQVAGAKIEGRKNLQIR 163  E+     K  PDK  +++ ++SG+ + GA +E R+NL IR Sbjct: 119 KEYQIATYK--PDKKTLKLKSGKHIEGATLEERRNLNIR 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 27

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 53> which encodes amino acid sequence <SEQ ID 54; NGS27>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Hejine)      Signal Score (−7.5): −5.45       Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:    calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)      count: 0 value: 1.80 threshold: 0.0      PERIPHERAL Likelihood = 1.80     modified ALOM score: −0.86 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----               bacterial cytoplasm --- Certainty = 0.559 (Affirmative) < succ> motifs: Subtilase_Asp (S, T, A, I, V)X(L, I, V, M, F)(L, I, V, M)D(D, S, T, A)G(L, I, V, M, F, C)x)                                              (A)x(L)(I)D(D)G(I)x{2}(D)            79: DDDFL                                       AALIDDGIVFD                       V

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS27 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 28

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 55> which encodes amino acid sequence <SEQ ID 56; NGS28>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.19    Possible cleavage site: 61 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 62 ALOM: Finding transmembrane regions (Klein et al.)    count:  0   value:   0.69 threshold:   0.0    PERIPHERAL Likelihood =  0.69   modified ALOM score:  −0.64 Score for OM-PP discrimination: −24.78 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −24.78 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space?  score: 2.47798 Periplasmic space?  score: 2.47798 ----- Final Results -----     bacterial periplasmic space --- Certainty= 0.916(Affirmative)     < succ>

The protein has homology with the following sequences in the databases: >prf||1306286A mobilization protein B [Escherichia coli] Length = 529 Score = 34.7 bits (78), Expect = 2.4 Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 12/69 (17%) Query: 344 QLRARQQEIPVDYARTAVCGRIPFRRHSRPTLRSRTLGAQRRRIVPNVGQAGGIRAD--- 400 +LRA  Q++P D+ +T V    P R   R   +    GA         GQ G IR D Sbjct: 440 RLRAAGQDLPADFVKTTVLDNTPIRWFYRAASQESRSGA---------GQTGEIRVDVER 490 Query: 401 RTPNTQRGT 409 R P  +RGT Sbjct: 491 RGPAGRRGT 499

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS28 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 29

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 57> which encodes amino acid sequence <SEQ ID 58; NGS29>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.61    Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  4.03 threshold:  0.0    PERIPHERAL Likelihood =  4.03   modified ALOM score:  −1.31 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.106(Affirmative) < succ>

The protein has homology with the following sequences in the databases: emb|CAB83930.1|(AL162753) hypothetical protein NMA0640 [Neisseria meningitidis Z2491] Length = 387 Score = 653 bits (1685), Expect = 0.0 Identities = 324/388 (83%), Positives = 351/388 (89%), Gaps = 1/388 (0%) Query: 1 MNITIAAPYCSLPSEPHFNRFWYLAELLSQSHDVLLITSNFKHYDKSFRRPEDAKAASQG 60 MNITI APYCSLPSEP+FNRFWYLAE LSQSHDVLLITS F+HYDKSFRR EDA A S G Sbjct: 1 MNITIVAPYCSLPSEPYFNRFWYLAERLSQSHDVLLITSRFRHYDKSFRRHEDAAATSNG 60 Query: 61 RLKVMLLEESGYSKNVSLGRVTSHHRFVKHFEKWLENCRPGEQDVVYSAYPLIATNLLLG 120 RL+V LL+E GY KNVSL RV SH  FV++  +WL + +  EQD+VYSAYPL+ATNLLLG Sbjct: 61 RLRVKLLDEPGYRKNVSLARVASHRVFVRNLARWLHSPQAAEQDIVYSAYPLMATNLLLG 120 Query: 121 KHKARLGYKLIVDVQDVWPESFSSVVPFLKKIPHNLLPFASRANRAYRYADALVAVSQTY 180 KHKARLGYKLIVDVQDVWPESFSSVVPFLKK+PH LLPFASRANRAYR ADAL+AVSQTY Sbjct: 121 KHKARLGYKLIVDVQDVWPESFSSVVPFLKKVPHKLLPFASRANRAYRCADALIAVSQTY 180 Query: 181 LDRAKEANPNVPGEVVYIGADFAAIAPPPRFRSKTVRFFYLGTLSYNYDVETVCKGVRKL 240 LDRAKEANPNVPGE VYIG DFAAIA PPRFRSKTVR FYLGTLSY+YDVETVCKGVRKL Sbjct: 181 LDRAKEANPNVPGETVYIGTDFAAIA-PPRFRSKTVRLFYLGTLSYSYDVETVCKGVRKL 239 Query: 241 LDDGENVELHIMGGGPDLDRLKQYACDGIKFYGYIPYAEMMSVAKGCDIAVNAIHSYAMQ 300 LDDGENVELHIMGGGPDL++LKQY    IKFYGY+PY+EMMS+AK CDIAVNAIHS+AMQ Sbjct: 240 LDDGENVELHIMGGGPDLEKLKQYENRAIKFYGYLPYSEMMSIAKACDIAVNAIHSHAMQ 299 Query: 301 SITNKLSDYMALQKPILNSQVHDEVAEVLTLLPHENYRSGDVDGFVQAAKDILKRKNDPV 360 S+TNKLSDYMALQKPILNSQ + EV ++L LLPHENYRSGDVD FVQAAK+ILKRK+DPV Sbjct: 300 SVTNKLSDYMALQKPILNSQNNAEVLDLLNLLPHENYRSGDVDSFVQAAKNILKRKDDPV 359 Query: 361 QSDEIVRRFRHDISYRKIVNLIERLANE 388 QSDEIVRRFR DISYRKIVNLIERLA+E Sbjct: 360 QSDEIVRRFRRDISYRKIVNLIERLAHE 387 >emb|CAB58324.1|(AL121855) hypothetical protein SCF62.09 [Streptomyces coelicolor A3 (2)] Length = 407 Score = 54.7 bits (130), Expect = 2e-06 Identities = 57/243 (23%), Positives = 105/243 (42%), Gaps = 24/243 (9%) Query: 99 RPGEQDVVYSAYP---LIATNLLLGKHKARLGYKLIVDVQDVWPESFSSVVPFLKKIPHN 155 R G  DVV++  P   L    L L     R G + + D  D+ PE + S     K + + Sbjct: 81 RVGPVDVVHACNPPDLLFLPALWL----KRRGARFVFDQHDLIPELYLSRFGRGKDLLYR 136 Query: 156 LLPFASANRAYRYADALVAVSQTYLDRAKEANPNVPGEVVYIGA-----DFAAIAPPPR 210  +    R    YR AD ++A +++Y D A       P +V  ++      F  + P P Sbjct: 137 AVCALERWT--YRAADVVLATNESYKDVAIRRGGRRPDDVFVVRSAPATDRFQPVPPEPE 194 Query: 211 F-RSKTVRFFYLGTLSYNYDVETVCKGVRKLLDDGENVELH--IMGGGPDLDRLKQYA-- 265   R K     YLG +     V+   + + KL D+    + H   +G G   D + + + Sbjct: 195 LKRGKPHLLCYLGVMGPQDGVDYALRALAKLRDEVGRTDWHAVFVGSGDAFDAMVELSRS 254 Query: 266 ---CDGIKFYGYIPYAEMMSVAKGCDIAVNAIHSYAMQSIT--NKLSDYMALQKPILNSQ 320     + ++F G IP A++++      D+ ++      + ++  NK+ +YMA+ +PI++ Sbjct: 255 LGLDEQVRFTGRIPDADLVRHLSTADVCLSPDPRNPLNDVSTMNKVLEYMAMGRPIVSFD 314 Query: 321 VHD 323 + + Sbjct: 315 LRE 317

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS29 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 30

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 59> which encodes amino acid sequence <SEQ ID 60; NGS30>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −4.8    Possible cleavage site: 46 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  1.54 threshold:  0.0    PERIPHERAL Likelihood =  1.54   modified ALOM score:  −0.81 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.113(Affirmative) < succ>

The protein has homology with the following sequences in the databases: fastidiosa (strain 9a5c) gb|AAF84279.1|AE003977_2 (AB003977) conserved hypothetical protein [Xylella fastidiosa] Length = 376 Score = 73.6 bits (179), Expect = 3e−12 Identities = 82/354 (23%), Positives = 143/354 (40%), Gaps = 35/354 (9%) Query: 1 MKIILTTSMSGLGGTETATVRLGRLLKRHGHDIILASSDG-PFVGEAQASGIRWQPVDFY 59 MKI+ T + +G GG E    R    ++  GH + L    G P    A+ +G+    ++ + Sbjct: 1 MKILHTEAATGCGGEEIYIYRHMLSMQAQGHHMALLCQPGAPLSTMARNAGLPVYHINMH 60 Query: 60 RGGLAGYLKSTFAYARMLRREQPDIIDCQMARVVPACALAAKIVSPKTKIICHSHGLDAA 119   G    L        +L+RE  D+++          A AA++   +T++I  S  L A Sbjct: 61 --GPWRVLNGIHTVQHLLQRETFDVVNTTSHVDTLIAAAAARLT--RTRLIVRSRHLMAP 116 Query: 120 TYPKTAKLFDKLGAYIIGNCICHEREKLIRHGFPAGRIAYA---------YNTPPEFHFRK 170    K+   +  L   +I   +H R+ LI+ G    RI             +T PE  +++ Sbjct: 117 I--KSQLTYTYLPHRVITVSQHRDLLIKQGIQPTRIGIVPPITA-QPPWMDTDPEHAWQR 174 Query: 171 TEK-------------ECAVLGTLSRLDTRAVHLMLDILKKMVGRNIPVRLNMAGIGEE 217 ++                ++G ++ L   +    +LD +  +   N  + L +AG GE Sbjct: 175 LQQTRHVVRTELGFNDNDIIVGCVAVLREAKGHRELLDAIAPLCQANPRLHLVIAGDGEP 234 Query: 218 -MDNLKAQAKRLGIEDKVTFLGGVRDLTGYFKEVDILVNTPHCVGDHGAGVGNNILEAGL 276  M +L A  K L +E ++  LG   D        DI       +       G   LEA Sbjct: 235 VMQHLLAHRKTLTLETQIHLLGYRHDAPRLMSGFDIFA-----LATQKEAAGTVFLEAAQ 289 Query: 277 YDTPVVTYNMAGISEMVITGQTGYCIPFGDDEAFIEAVDTLIKHPELRSQNGKA 330    P++   + G+ EM+  G     +  G+  A   A+ TL+ + + R  MG+A Sbjct: 290 AGIPIIATRVGGVPEMLQEGTNAILVTPGNQTALTNALHTLVTNNQQRHSMGRA 343

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS30 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 31

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 61> which encodes amino acid sequence <SEQ ID 62; NGS31>. Analysis of this protein sequence reveals the following: GvH:  Examining signal sequence (von Heijne)     Signal Score (−7.5): −5.36 Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  3.50 threshold:  0.0    PERIPHERAL Likelihood =  3.50   modified ALOM score:  −1.20 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.299(Affirmative) < succ>

The protein has homology with the following sequences in the databases: gb|AAB49297.1|(U84350) hypothetical hydroxylase a [Amycolatopsis orientalis ] Length = 491 Score = 111 bits (278), Expect = 1e−23 Identities = 87/269 (32%), Positives = 123/269 (45%), Gaps = 15/269 (5%) Query: 1 LKNGAAFSWGSRYTEFDF----TDKFSDGPGTVYQVRRAVRDKILIEEAAKQGVEVRFGH 56 +K G  F WG+R   + F    + K +      YQV RA FD IL++ A  +GV VR G Sbjct: 73 IKRGGTFRWGARPEPWTFHFGISAKMAGSTSHAYQVERAKFDDILLKNAKSKGVVVREGC 132 Query: 57 GVTAFDNSGDFARLNIETDT-GESYELTAKFVLDASGY-GRVLPRLLNLETPSHLPPRQT 114  V      G+       TD  G ++E++A+FV+DASG   R+  ++      S Sbjct: 133 SVNDVVEDGERVTGARYTDADGNAHEVSARFVIDASGNKSRLYTKVNGRNYSEFFRSLA 192 Query: 115 HFTHIDDNITHPKFDRNKILITTHPQHRDVWIWLIPFGDNRCSVGVV---GTPKLAGES 171  F + +     P+     IL          W W I P  D   SVG V      DK+ G+ Sbjct: 193 LFGYFEGGKRLPEPVSGNILSVAFDSG---WFWYIPLSDTLTSVGAVVRREDADKIQGDR 249 Query: 172 ETVLKKFVYECPHLSEILDKAVWENDFPFRSIQ---GYSANVKSLHGEHFALLGNAAEFL 228 E  L   + ECP++SE L  A       +  ++    YS    S        L+G+AA F+ Sbjct: 250 EKALNTLIAECPLISEYLSNATRVTRYGELRVRKDYSYQQDSYWRPGMVLVGDAACFV 309 Query: 229 DPVFSSGVTIALHSAELAADLLTKQLKGE 257 DPVFSSGV +A +SA LAA  +   L G+ Sbjct: 310 DPVFSSGVHLATYSALLAARSINSVLAGD 338

A homolog (amino acids 280-341) was found in serogroup A N.meningitidis but not in serogroup B, so NGS31 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 32

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 63> which encodes amino acid sequence <SEQ ID 64; NGS32>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.49    Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.80 threshold:  0.0    PERIPHERAL Likelihood =  7.80   modified ALOM score:  −2.06 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.278(Affirmative) < succ>

The protein has homology with the following sequences in the databases: fastidiosa (strain 9a5c) gb|AAF83310.1|AE003899_2 (AE003899) phage-related repressor protein [Xylella fastidiosa] Length = 143 Score = 87.0 bits (214), Expect = 2e−16 Identities = 40/71 (56%), Positives = 54/71 (75%) Query: 1 MFSGEQLGQAISEAIKRKNVSQKEVADHFGVKQPSVSGWIKNGRIDKKHLDKLIDYFSDV 60 M +GEQLG+AI +A++ K V+  ++A+HFGVK PSV GWIK GRI K+ L  L  YFSDV Sbjct: 1 MLTGEQLGRAIKQAMQLKGVTPTKMAEHFGVKAPSSVYGWIKEGRISKEKLPSLWSYFSDV 60 Query: 61 VTPSHFGIETF 71 V P+H+G+E + Sbjct: 61 VGPTHWGLEAW 71 >sp|P18680|RPC1_BPHK0 26 KD REPRESSOR PROTEIN (REGULATORY PROTEIN CI) emb|CAA34222.1|(X16093) cI gene product (AA 1-208) [Bacteriophage HK022] Length = 235 Score = 80.5 bits (197), Expect = 2e−14 Identities = 60/200 (30%), Positives = 99/200 (49%), Gaps = 15/200 (7%) Query: 22 QKEVADHFGVKQPSVSGWIKNGRIDKKHLDKLIDYFSDVVTPSHF--------GIETFRV 73 Q ++A    V   ++S W     1 +K  DK+    S +  T + +        GI    + Sbjct: 29 QADLARLKVTPKAISKFNGESIPRK--DESLASVLGTTAAYLHGYADDDGITVNHL 86 Query: 74 LKSNEQSSIRFPRLNAEATCGAGT-INDHYIEVVDYVTVAAAWAREKLGGNLNK-IQVIT 131  +SN+    R   L+ +A+ G GT +++ +IE +  +      AR    G   + ++VIT Sbjct: 87 SRSNDY--YRVDVLDVQASAGPGTMVSNEFIEKIRAIEYTTEQARILFNGRPQESVKVIT 144 Query: 132 ARGDSMEPTIENGDVMFVDTAVEAFDGDGLYLLWYIDGLKAKRLQSTVGGGLMIISDNSS 191  RGDSME TI  GD +FVD ++  FDGDG+Y+  Y   +  KRLQ      L +ISDN++ Sbjct: 145 VRGDSMEGTINPGDEIFVDVSITCFDGDGIYVFVYGKTMHVKRLQMQ-KNRLAVISDNAA 203 Query: 192 YRTETVRGEDLNAVRIIGRI 211 Y    +   +   + I+ ++ Sbjct: 204 YDRWYIEEGEEEQLHILAKV 223

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 33

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 65> which encodes amino acid sequence <SEQ ID 66; NGS33>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.87    Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  4.88 threshold:  0.0    PERIPHERAL Likelihood =  4.88   modified ALOM score:  −1.48 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.313(Affirmative) < succ>

The protein has homology with the following sequences in the databases: gb|AAF31132.1|(AF069529) Gp54 [Bacteriophage HK97] Length = 273 Score = 47.4 bits (111), Expect = 3e−04 Identities = 33/123 (26%), Positives = 52/123 (41%), Gaps = 20/123 (16%) Query: 221 NGGLSGKPKNANVPRRRKTHGVPLQEIADLYNEVLGGRLPSVQVLNDTRKRAIANRWCEM 280 NGG  G+ K    P RRK   +  +   + YN  +G RLP    +N+ RKR +  + Sbjct: 160 NGGGDGQVK----PERRKAERIDYESFLNAYNTEVGDRPHAVAVNEKRKRRL-KKIIPQ 214 Query: 281 LGTAAPNGKVRFGDKETGIAFAGFFRKVA--MNPFWMGENQTGFAVGFDWIFKAGNFVK 338 L T   +G             F  + R       PF+ G+N TG+ FD++ +  + Sbjct: 215 LKTPNVDG-------------FRAYVRAFVHQAKPFYFGDNDTGWTADFDYLLREDSLTG 261 Query: 339 ILE 341 + E Sbjct: 262 VRE 264

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 34

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 67> which encodes amino acid sequence <SEQ ID 68; NGS34>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.65    Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  3.76 threshold:  0.0    PERIPHERAL Likelihood =  3.76   modified ALOM score:  −1.25 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.310(Affirmative)       < succ>     bacterial periplasmic space --- Certainty= 0.000(Not Clear)     < succ>      bacterial outer membrane --- Certainty= 0.000(Not Clear)      < succ>      bacterial inner membrane --- Certainty= 0.000(Not Clear)      < succ>

The protein has homology with the following sequences in the databases: >pir||H82649 hypothetical protein XF1674 XF1569 [imported]- Xylella fastidiosa (strain 9a5c) gb|AAF84378.1|AE003986_8 (AE003986) hypothetical protein [Xylella fastidiosa] gg|AAF84483.1|AE003993_2 (AE003993) hypothetical protein [Xylella fastidiosa] Length = 316 Score = 167 bits (424), Expect = 2e−40 Identities = 108/308 (35%), Positives = 152/308 (49%), Gaps = 30/308 (9%) Query: 10 ETSVIRSLSSASLYMFTRRMFYQRRGYVWQRANHHAPICNLERVFTIGETKRLIINIPPR 69 E +VI++   A    FTR F QR+   ++   HH I   ++ V  G  K ++IN+PP Sbjct: 10 EQAVIKARCEADHLFFTRYFFKQRQQLRFRVNWHHHVIAGVVDDVIAGRRKDVVINVPPG 69 Query: 70 YSKTEIAVVNFIAWAMGRVPDCEFIHASYSAALAVNNSVQIRNLVQHEEYRAIFP-DLAL 128  SKTE+  +N +A  +   P   F+H SYS  LA+ NS   R +VQ +EYRA++P ++A Sbjct: 70 SSKTELVAINVMARGLALNPYARFLHISYSDDLALLSETAREIVQSDEYRALWPLEIAD 129 Query: 129 AGESGHHWKTT-----AGGVMYXXXXXXXXXXXXXXRHREGFGGCIIIDDPHKADEARSE 183   +S   W        AGGV Y                  G+ G IIIDDP K ++A S+ Sbjct: 130 DAKSKKRWVVDGKKAGGV-YAVSLGGQVTGFRAGHAPGWQGAIIIDDPLKVEDAYSK 188 Query: 184 VRRQNVIDWFQNTVESRKNSPDTPIILIMQRLHEKDLAGWLLDGGNGEEWEHLCLPAIQE 243   R        +TV+SRK SPDTPII+IMQRL + D  G++  GG    WE + +PA+ + Sbjct: 189 TGRSKANRKLVSTKSRASPDTPIIVIMQRLAQDDPTGFIQSGGFPGAWECIEIPALID 248 Query: 244 DG-----------------------TALWPEKHDIETLRREQAAPWFAGQYLQKPAPP 280 D                         + WP K  +  L  +E    YVF+GQY Q+P+P Sbjct: 249 DAYVSRLPEHVQGQVVRDAQDQDGRYSYWPYKEPLAELLALEATDRYVFSGQYQQRPSPL 308 Query: 281 DGGTFKPD 288  GG  K D Sbjct: 309 GGGIIKGD 316

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 35

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 69> which encodes amino acid sequence <SEQ ID 70; NGS35>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −1.07    Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  1.64 threshold:  0.0    PERIPHERAL Likelihood =  1.64   modified ALOM score:  −0.83 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.020(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_047925.1|gp34 [Bacteriophage phi-C31] emb|CAA07104.1|(AJ006589) gp34 [Bacteriophage phi-C31] Length = 457 Score = 59.7 bits (143), Expect = 1e−07 Identities = 68/272 (25%), Positives = 117/272 (43%), Gaps = 49/272 (18%) Query: 226 GYSPVEQIIMTVNIALKRQVHALEYYTAGSVPDALVGVPETWSADDIRRFQEYWDLLLSG 285 G SP+     +++ AL  Q +  +++  G++P A+V VP T S + + R +E W    SG Sbjct: 192 GCSPISYARESIGLALAAQKYGSKFFANGGAMPGAVVEVPGTMSKEGLARAREAWRAANSG 251 Query: 286 -----------ETAQRRKMRFVPGELSRNFRETRQPPLKDVYDEWLARVVCFAFSVEPTP 334            E A+  K+   P E    F +T+Q  + ++     AR+    F V P Sbjct: 252 VDNAHRVALLTEGAKFSKVAMSPDEAQ--FLQTRQFQVPEI-----ARI----FGVPPH- 299 Query: 335 FVAQVNRSVAETS--REQSLSDGMGSLKNWVKALIDDVLARYMDMAA--YEFVWKGEESL 390  ++    S +  S   EQ+++  M SL+ W++ +            A  + FV    + + Sbjct: 300 LISDATNSTSWGSGLAEQNIAFTMFSLRPWLERIEAGFNRLLFAETADRFRFVKFNLDEI 359 Query: 391 N---PKEQAEIYAIYKNAGILTADEIRAELGKEPLP-GQG--------------QPEPDK 432     PKE+ E++++    GI + DE+RA     PLP G G              +PEP+ Sbjct: 360 KRGAPKERMELWSLGLQNGIYSIDEVRAAEDMTPLPDGLGEKYRVPLNLGEVGEEPEPEP 419 Query: 433 QDG----RKPEEPPNQGAEKLGKSESPMSEDE 460          P E P++  E  GK +   + +E Sbjct: 420 APAPPAIEPPAEEPDEEPEPEGKPDDEGATEE 451

A homolog (amino acids 641-700) was found in serogroup A N.meningitidis but not in serogroup B, so NGS35 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 36

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 71> which encodes amino acid sequence <SEQ ID 72; NGS36>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 4.3    Possible cleavage site: 26 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 27 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:   1.70 threshold:  0.0    PERIPHERAL Likelihood =   1.70   modified ALOM score:   −0.84 Score for OM-PP discrimination:  0.02 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination:  0.02 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane?  score: 0.00213559 Outer membrane?  score: 0.00213559 ----- Final Results -----     bacterial outer membrane --- Certainty= 0.232(Affirmative)     < succ>

The protein has homology with the following sequences in the databases: >pir||D82437 TonB receptor-related protein VCA0625 [imported]-Vibrio cholerae (group O1 strain N16961) gb|AAF96526.1|(AE004392) TonB receptor-related protein [Vibrio cholerae] Length = 784 Score = 103 bits (256), Expect = 2e−20 Identities = 104/427 (24%), Positives = 162/427 (37%), Gaps = 100/427 (23%) Query: 31 NTEQQKELNTIVVHGKRS-ADQKGADDVYYKNVSNAYVGKEYLERYRVQSAGDVLKGLNG 89 NTEQ  +  T+ VHG+    DQ+   D               L++ R  +  D+  G+ Sbjct: 57 NTEQAVD-ETVTVHGQSILTDQRTRSD---------------LDkVRGIANADIFSGITS 100 Query: 90 VYNMNTRTAGGAITPNIRGITGKGRIPVTIDGTEQTIDVWMNNYGVGDRNYLDPALFRSI 149 V + N     GA+   IRG+ G+GR+P+ IDG+ Q+        GV DR Y+D  L  S+ Sbjct: 101 VQSNNMHNEAGALDIGIRGVQGEGRVIFIDGSLQSTHTSRGYQGVSDRTYIDTDLLSSL 160 Query: 150 AVEKSPALTRG--VKSGVGGAMSIRTIEPSDIIPEGRNWGIEVKTEFSGNTVAQKNDLRQ 207  V K   +         VGG ++  T+   DII + + +G+ +K Sbjct: 161 TVNKGATIESSPYASGAVGGVVNATTLGIKDIIKDDQAFGVVLK---------------- 204 Query: 208 FLGRDYRTLSPIGATADGVSGMPDVLTGYTGKPSPTALLLDEGIADTKFSGGKSHTNFKD 267 A A+  +  PDV   Y+ +       LDE    + F  G Sbjct: 205 -------------ARANNHNRTPDVSGDYSEQGQ---YALDERGEHSAFKHG-------- 240 Query: 268 DRQLMLSAAFKTDITDGLAAYSHRQKGNYYAGKRGYQSYLNNPI--YGADACYDQYPDKS 325    LML   ++ +  + + AYS R KGN++AGK+GY+ Y   P+   G +     +   S Sbjct: 241 --SLMLGLGYQAESFTVLAYSKRSKGNHFAGKKGYEEY-QEPVVGQGQEVVNTSFESDS 297 Query: 326 WREKDILCKSASLVPNMAVLFRPGEEIMNSHTDTKILLLKNNWYLPDNQKISLQYMDNK 385 W  K     S      N    +R        H      +L   WY          Y D K Sbjct: 298 WLFK---LASDTGTAHNADFNYR--------HHAQKAGEVLMAYWYKSSEDWEGNPYPDGK 347 Query: 386 IGFGEINPLITAWILGFAEQSLNEPVQQAPGIGTKIDSKTYKIGYEWKPQNNKWIDLQAD 445          +  W LG A+ +                  TY   Y ++P ++ W++L A+ Sbjct: 348 -------DRMPQWGLGTAKVN------------------TYSANYYYQP-DHPWLNLNAN 381 Query: 446 MWRVKTD 452  W  + D Sbjct: 382 FWYTEAD 388 Score = 94.7 bits (234), Expect = 5e−18 Identities = 80/290 (27%), Positives = 126/290 (42%), Gaps = 37/290 (12%) Query: 929 SYDLDNHLFARYASRFPSLYELTAATGSGGLYGSETVAEYS----LKPEKSTNWEV 984 +Y L  + +LF + +R  R PSLYE T          S  V  Y+    +KPE++ N EV Sbjct: 514 TYALTPSTQLFLKSSRTYRMPSLYETTL---------SNEVFSYNPYNPIKPEQAWNNEV 564 Query: 985 GYNFNFAPHFAKLRQGDLRLTYYSNKIKNQIDTSN--EDGGMIQ---------YDKAVSK 1033 G  F  +    +  + +L ++Y+ N IK+ I      +  GM +         YDK Sbjct: 565 GVQFMASNSVLQDDRLNLSVSYFRNSIKDFISGGRLAKTPGMSEWQANFTFTNYDKLQLS 624 Query: 1034 GVELQSRLDSGRFFASFGGTYRLKHMVCDKGIAFKFDYYLQRVPECLEGGFGLSRFFQSL 1093 G EL +       +  F  T   +  +C    A            C   GF        + Sbjct: 625 GWELGAHYQYAWILYTHPAATLYSETKICSVQQA-----QYAESDTCNSLGFAWGLTPTRI 679 Query: 1094 QPKYSLTLDVGTRFFNEKLELGMRAIHHSKAERRNYDKLIADGAGQVYARNGKPYGWHAA 1153  PK +L L+VGT+FFN+ L+ G++  +HS   + N    +A  A          Y Sbjct: 680 PPKQNLYLNVGTKFFNDTLDSGVSYHSG--KSNPSDWLAGTAANPILEIPSDY----- 732 Query: 1154 TLLDAYARYRIGKHIDLNFSVTNLANRYYLDPMSSTPVPGPGRTITFGIK 1203   +D Y++Y +  +  L F++ N+ +RY + P S   +P PGRTIT G + Sbjct: 733 -TIDLYSQYELNANTQIFFAINNVTDRYQVRPGSVVSMPDPGRTITLGFE 781

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 37

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 73> which encodes amino acid sequence <SEQ ID 74; NGS37>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 4.47    Possible cleavage site: 21 >>> Seems to have a cleavable N-term signal seq. Amino Acid composition of Predicted Mature Form:  calculated from 22 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.21 threshold:  0.0    PERIPHERAL Likelihood =  7.21   modified ALOM score:  −1.94 Score for OM-PP discrimination: 16.42 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 16.42 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane?  score: 1.64214 Outer membrane?  score: 1.64214 ----- Final Results -----     bacterial outer membrane --- Certainty= 0.938(Affirmative)     < succ>

The protein has homology with the following sequences in the databases: >sp|Q03155|AIDA_ECOLI ADHESIN AIDA-I PRECURSOR pir||S28634 adhesin AIDA-I precursor-Escherichia coli plasmid pIB6 emb|CAA46156.1|(X65022) AIDA-I [Escherichia coli] Length = 1286 Score = 35.8 bits (81), Expect = 0.67 Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 16/138 (11%) Query: 3 ASQLTLAVLLAAAFGSAYAVEVKGGDSSKGQLIQAAESDFLPFGSGAADIKVSTGNGLSK 62 A    L + + + G+A+AV + G  SS G  + + E+  +  G G ++  V++G   ++ Sbjct: 31 AKNTLLVLAWSTIGNAPAVNISGTVSS-GGTVSSGETQIVYSGRGNSNATVNSGG-TQ 87 Query: 63 SINLEAGPAQRIRNKYGNAPINGGNQNTNVNGAANSRYLQPGDINPIA--GWFSKTRLA- 119  +N          N       + G+QN   +GA  S  +  G I  ++  G  S T L+ Sbjct: 88 IVNNGGKTTATTVN-------SSGSQNVGTSGATISTIVNSGGIQRVSSGGVASATNLSG 140 Query: 120 ---QVWYEKRANNTEVFS 134     ++    A+NT +FS Sbjct: 141 GAQNIYNLGHASNTVIFS 158

The protein was expressed in E.coli as an insoluble 32.45 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 38

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 75> which encodes amino acid sequence <SEQ ID 76; NGS38>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.34    Possible cleavage site: 24 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 25 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  3.98 threshold:  0.0    PERIPHERAL Likelihood =  3.98   modified ALOM score:  −1.30 Score for OM-PP discrimination: 2.87 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 2.87 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane?  score: 0.287446 Outer membrane?  score: 0.287446 ----- Final Results -----     bacterial outer membrane --- Certainty= 0.607(Affirmative)     < succ>

The protein has homology with the following sequences in the databases: >sp|Q03155|AIDA_ECOLI ADHESIN AIDA-I PRECURSOR pir||S28634 adhesin AIDA-I precursor-Escherichia coli plasmid pIB6 emb|CAA461S6.1|(X65022) AIDA-I [Escherichia coli] Length = 1286 Score = 35.8 bits (81), Expect = 0.67 Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 16/138 (11%) Query: 3 ASQLTLAVLLAAAFGSAYAVKGGDSSKGQLIQAAESDFLPFGSGAADIKVSTGNGLSK 62 A    L + + +  G+A+A+V + G  SS G  + + E+  +  G G ++  V++G   ++ Sbjct: 31 AKNTLLVLAVVSTIGNAFAVNISGTVSS-GGTVSSGETQIVYSGRGNSNATVNSGG--TQ 87 Query: 63 SINLEAGPAQRIRKYGNAPINQGNQNTNVNGAANSRYLQPGDINPIA--GWFSKRLA- 119  +N          N       + G+QN   +GA  S  +  G I  ++  G  S T L+ Sbjct: 88 IVNNGGKTTATTVN-------SSGSQNVGTSGATISTIVNSGGIQRVSSGGVASATNLSG 140 Query: 120 ----QVWYEKRANNTEVFS 134     ++    A+NT +FS Sbjct: 141 GAQNIYNLGHASNTVIFS 158 >pir||G81213 conserved hypothetical protein NMB0313 [imported]-Neisseria meningitidis (group B strain MD58) gb|AAF40758.1|(AE002388) conserved hypothetical protein [Neisseria meningitidis MC58] Length = 488 Score = 84.3 bits (207), Expect = 3e−15 Identities = 111/498 (22%), Positives = 185/498 (36%), Gaps = 35/498 (7%) Query: 7 LLFLPLCTVCLAAPSNDAADERRRLLDEGSRQTQQYRESGW--LDTEQARGEVEENDGY 64 +L LPL        S   A+E  R  D  SR   +  E+    +D E+  G+V E    + Sbjct: 19 MLLLPLLA------SAAYAEETPREPDLRSRPEFRLHEAEKPIDREKPGQVREKGKVL 72 Query: 65 SIGGEIYQVGDTAEELESAIYHALNARQWHKVRQFAARYAKLPRHKPALIHLADALQKRD 124  I GE        E L  A+Y A+ +     +R     Y +  +    L   A  +  + Sbjct: 73 QIDGETLL--KNPELLSRAMYSAVVSNNIAGIRVILPIYLQQAQQDKMLALYAQGILAQA 130 Query: 125 EGDFRAAGNSFQTALEAEPDNPRLLLEAGRFYAEDNQNKESAAAFEKVLKTDIPAETRPI 184 +G  + A + ++  + A+PD P + +       E+ QN+ +A   F+++   ++P + Sbjct: 131 DGRVKEAISHYRELIAAQPDAPAVRMRLAAALFENRQNEAAADQFDRLKAENLPPQLMEQ 190 Query: 185 VENYLSELGKRRRWHGQISLGYGYNSNVNQGNGINQCVWEIAGMCLMERTLPAPTDSTFS 244 VE Y   L +R  W            N+NQ     Q           + T P   D T Sbjct: 191 VELYRKALRERDAWKVNGGFSVTREHNINQAPKRQQ---------YGKWTFPKQVDGTAV 241 Query: 245 SYSATAEKTVPLKGNHGVQVRGVLYGNRYTEKDKDSAAMPDYGYNGSLYAGYAYADARS 304 +Y   AEK   LK        G + G  Y    K       +      +  G  +AD R Sbjct: 242 NYRLGAEKKWSLKNGWYTTAGGDVSGRVYPGNKK-------FNDMTAGVSGGIGFADRRK 294 Query: 305 SFSLLPYFEYDFRNRHTHYRAWGADADWSRTLSPHNRINSHAGAKKTGYGGQSKTYFADF 364    L  + E        +    GA   ++R  +P W+  S A   + G    ++   +D Sbjct: 295 DAGLAVFHERRTYGNDAYSYTNGARLYFNRWQTPKWQTLSSA---EWGRLKNTRRARSDN 351 Query: 365 KQYELGAGAEFSITLKSGLLVNFDAAPKAYP-EKSSSSKEYTARLGAYRLFSGGTYLNAV 423    ++     F    +   +   D  R+  P ++  +   Y  R  A+    GG+ L+++ Sbjct: 352 THLQISNSLVFYRNARQYMGGLDFYRERNPADRGDNFNRYGLRF-AWGQEWGGSGLSSL 410 Query: 424 LLY--RRSLYDAASFVSDNK--RRRDKQYIMMAAAGFPQWNIKGVYPELRFRRTIAHSNA 479 L     +  Y+   F S  K  RRRDK+     +      + KG+ P L        SN Sbjct: 411 LRLGAAKRHYEKPGFFSGFKGERRRDKELNTSLSLWHRALHFKGITPRLTLSHRETRSND 470 Query: 480 VYYRYRQNEWLLGFKYRF 497 V+  Y +N   +F   F Sbjct: 471 VFNEYEKNRAFVEFNKTF 488 >pir||C81790 conserved hypothetical protein NMA2174 [imported]- Neisseria meningitidis (group A strain Z2491) emb|CAB85386.1|(AL162758) conserved hypothetical protein [Neisseria meningitidis Z2491] Length = 490 Score = 84.0 bits (206), Expect = 4e−15 Identities = 111/498 (22%), Positives = 185/498 (36%), Gaps = 35/498 (7%) Query: 7 LLFLPLCTVCLAAPSNDAADERRRELLDEGSRQTQQYRESGW--LDTEQARGEVEENDGYI 64 +L LPL        S   A+E  R  D  SR   +  E+    +D E+  G+V E    + Sbjct: 23 MLLLPLLA------SAAYAEETPREPDLRSRPEFRLHEAEVKPIDREKVPGQVREKGKVL 74 Query: 65 SIGGEIYQVGDTAEELESAIYHALNARQWHKVRQFAARYAKLPRHKPALIHLADALQKRD 124  I GE        E L  A+Y A+ +     +R     Y +  +    L   A  +  + Sbjct: 75 QIDGETLL--KNPELLSRAMYSAVVSNNIAGIRVILPIYLQQAQQDKMLALYAQGILAQA 132 Query: 125 EGDFRAAGNSFQTALEAEPDNPRLLLEAGRFYAEDNQNKESAAAFEKVLKTDIPAETRPI 184 +G  + A + ++  + A+PD P + +       E+ QN+ +A  F+++   ++P + Sbjct: 133 DGRVKEAISHYRELIVAQPDAPAVRMRLAAALFENRQNEAAADQFDRLKAENLPPQLMEQ 192 Query: 185 VENYLSELGKRRWHGQISLGYGYNSNVNQGNGINQCVWEIAGMCLMERTLPAPTDSTFS 244 VE Y   L +R  W            N+NQ     Q           + T P   D T Sbjct: 193 VELYRRKALRERDAWKVNGGFSVTREHNINQAPKRQQ---------YGKWTFPKQVDGTAV 243 Query: 245 SYSATAEKTVPIKGNHGVQVGVLYGNRYTEKSDYGYRNGSLYAGYAYADARS 304 +Y   AEK   LK        G + G  Y    K       +      +  G  +AD R Sbjct: 244 NYRLGAEKKWSLKNGWYTTAGGDVSGRVYPGNKK-------FNDMTAGVSGGIGFADRRK 296 Query: 305 SFSLLPYFEYDFRNRHTHYRAWGADADWSRTLSPHRINSHAGAKKTGYGGQSKTYFADF 364    L  + E        +    GA   ++R  +P W+  S A   +G    ++   +D Sbjct: 297 DAGLAVFHERRTYGNDAYSYTNGARLYFNRWQTPKWQTLSSA---EWGRLKNTRRARSDN 353 Query: 365 KQYELGAGAEFSITLKSGLLVNFDAARKAYP-EKSSSSKEYTARLGAYRLFSGGTYLNAV 423    ++     F    +   +   D  R+  P ++  +   Y  R  A+    GG+ L+++ Sbjct: 354 THLQISNSLVFYRNARQYWMGGLDFYRERNPADRGDNFNRYGLRF-AWGQEWGGSGLSSL 412 Query: 424 LLY--RRSLYDAASFVSDNK--RRRDKQYIMMAAAGFPQWNIKGVYPELRFRRTIAHSNA 479 L     +  Y+   F S  K  RRRDK+     +      + KG+ P L        SN Sbjct: 413 LRLGAAKRHYEKPGFFSGFKGERRRDKELNTSLSLWHRALHFKGITPRLTLSHRETRSND 472 Query: 480 VYYRYRQNEWLLGFKYRF 497 V+  Y +N   + F   F Sbjct: 473 VFNEYEKNRAFVEFNKTF 490

The protein was expressed in E.coli as an insoluble 52.03 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 39

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 77> which encodes amino acid sequence <SEQ ID 78; NGS39>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.38    Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.16 threshold:  0.0    PERIPHERAL Likelihood =  7.16   modified ALOM score:  −1.93 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.325(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_052685.1|serine protease EspP [Eseherichia coli] pir||T00317 probable serine proteinase espP, extracellular-Escherichia coli plasmid pO157 pir||T42120 probable serine proteinase espP, extracellular-Escherichia coli plasmid pO157 emb|CAA66144.1|(X97542) putative exoprotein-precursor [Escherichia coli] dbj|BAA31836.1|(AB011549) serine protease EspP [Escherichia coli] gb|AAC70088.1|(AF074613) putative exoprotein-precursor [Escherichia coli O157:H7] Length = 1300 Score = 58.9 bits (141), Expect = 2e−07 Identities = 153/687 (22%), Positives = 248/687 (35%), Gaps = 106/687 (15%) Query: 194 DLTVENKTLSDA---EFGVYALNTSMVNLSSKDNNEVKSTQVGLYSQDGGSINVDR--- 247 D     +NT +DA      Y  N ++ +LS  D  E  + + G    +    +V R Sbjct: 595 DYVAGMQNTEADAVKQNGNAYKTNNAVSDLSQPDW-ETGTFRFGTLHLENSDFSVGRNAN 653 Query: 248 --------KDNIIEGDAVALVGKGGSQNIRAS----RTLISSKSLGIHAEQAAKIAITG 295         K NI  GD  A +     +NI       R N++   S G   E      IT Sbjct: 654 VIGDIQASKSNITIGDTTAYIDLHAGKITGDGFGFRQNIVRGNSQG---ETLFTGGITA 710 Query: 296 ASNTIHASNAAIRSLDKSEVKIDGQITIDSNVANLARQDGSIH---LNYKDDTRITGATV 352   +TI   + A          ++ + TI+ N A++  Q G      ++   +  +TG Sbjct: 711 EDSTIVIKDKAKALFSNYVYLLNTKATIE-NGADVTTQSGMFSTSDISISGNLSMTGNPD 769 Query: 353 SDKGLVAIKPLNNTNIVADTIHYKGDVLAVNKGKVELDF----TPNILLAGRLDNFSGLT 408  D        LN+ + +      +  ++A NK  V  D     + +I+      + S L+ Sbjct: 770 KDNKFEPSIYLNDASYLLTPDSAR--LVMASWGPIHSTKSASIMPGHDESPLSQLS 827 Query: 409 DSKHKNLFENYVANLDSKSAGEINFNLAKDAL----WTMTGQSWLDKLEGQGTIDFNNDA 464 D   K L    +   D    G +N   A   +    W +TG S L  L+   ++ +  D+ Sbjct: 828 DRTSKGLALGLLGGFDVSYRGSVNAPSASATMNNTWWQLTGDSALKTLKSTNSMVYFTDS 887 Query: 465 KTSGR--ALHIGELAGANK-FLMHLNKDGIHSDMLYVKKGTSTPQEVVVKNLSEVLDSMN 521   + +   L + ELA +N  + M  N     SD L VKK  S    ++   L + L Sbjct: 888 ANNKKFHTLTVDELATSNSAYAMRTNLS--ESDKLEVKKHLSGENNIL---LVDFLQKPT 942 Query: 522 YGERLRFATVTNSKNEFVNGKKYIDDTHLMEDALTVEYSAHNGXXXXXXXXXXSFNGSEM 581   ++L    V+  K+   N  K    T    D   V Sbjct: 943 PEKQLNIELVSAPKTNENFKASKQTIGFSDVTPV------------------------ 978 Query: 582 TAEKAGDPYVNKTYTDNRQNVYLVKQATGNPSRNVKNINDMFDSTAHYAFT--LDTYAKR 639    +  DD +  T++    N    K+AT N +           S  + AF   ++   KR Sbjct: 979 ITTRETDDKI--TWSLTGYNTVANKEATRNAAA--------LFSVPYKAFLNEVNNLNKR 1028 Query: 640 EGERAFSTLDKKEGDWIRLTHTRVIQSNAFRFHNNDFEIGYDRFSLNEQEKKRKWGISLD 699  G+     ++ + G W R+       S  F  +    ++G D+       K    G+ L Sbjct: 1029 MGD--LRDINGEAGAWARIMSGTGSASGGFSDNYTHVQVGVDK-------KHELDGLDLF 1079 Query: 700 YGHGRTSLWNTFGKD----KIRKYELALYNTTQYIDKEGDETGYIDNVLKIGKLRNRVIA 755  G   T   ++   D    K +     LY +  +     D   YID + K     N   A Sbjct: 1080 TGFTVTHTDSSASAFSGKTKSVGAGLYASAMF-----DSGAYIDLIGKYVHHDNEYTA 1134 Query: 756 RNHMGQLWGKGKYSNTLFSISTEYGRRKFLDDDKLWRITPQVQLQYSYLRGTGYRI-DNG 814     G   G   YS   +    E G R  + +D  W I PQ +L Y  + G  +   D G Sbjct: 1135 -TFAGL--GTRDYSTHSWYAGAEAGYRYHVTEDA-W-IEPQAELVYGSVSGKQFAWKDQG 1189 Query: 815 INVNLSHA--NSLIGRLGLDVVRKFDG 839 +++++     N LIGR G+DV + F G Sbjct: 1190 MHLSMKDKDYNPLIGRTGVDVGKSFSG 1216 Score = 36.6 bits (83), Expect = 1.2 Identities = 97/412 (23%), Positives = 164/412 (39%), Gaps = 83/412 (20%) Query: 63 DNIVTMKSGDADADYVNNSKVLTETPYYKSKRGSNGIFAYGDKSLVKLIGEIVK--SE 120 D V    G  +   ++ SK      Y  + +G   + A+   S V  + +N  +   +E Sbjct: 163 DKFVVETRGATEGADISLSKQQALERYGVNYKGEKKLIAFRAGSGVVSVKKNGRITPFNE 222 Query: 121 ISEKSKALNGGFRHIGIYS-W---QNAKVE----LSSKSDN--------------IVQGG 158 +S K + LNG F HI  +S W    N + +    ++++ D+              +V G Sbjct: 223 VSYKPEMLNGSFVHIDDWSGWLILTNNQFDEFNNIASQGDSGSALFVYDNQKKKWVVAGT 282 Query: 159 IWGLYS----NNSSISLKGKNNVISNPKYNVFAYKKAKVDLTVENKNTLSDAEFGVYALN 214 +WG+Y+     N +   K     I N K N ++Y    VD++     T+ + +  + Sbjct: 283 VWGIYNYANGKNHAAYSKWNQTTIDNLK-NKYSY---NVDMSGAQVATIENGK--LTGTG 336 Query: 215 TSMVNLSSKDNNEVKSTQVGLYSQ----DGGSINVDRKDNIIEGDAVALVGKG-----GS 265 +   ++ +KD        + L S      GG +  D+K   + GD     G G     GS Sbjct: 337 SDTTDIKNKDLIFTGGGDILLKSSFDNGAGGLVFNDKKTYRVNGDDFTFKGAGVDTRNGS 396 Query: 266 Q---NIR-ASRTNL--ISSKSLGIHAEQAAK------IAITGASNTIHASNAAIRSLDKS 313     NIR  ++ NL  I   +L +   Q         + I GA  T   +N  I S D Sbjct: 397 TVEWNIRYDNKDNLHKIGDGTLDVKTQNTNLKTGEGLVILGAEKTF--NNIYITSGD-G 453 Query: 314 EVKIDGQITIDSNVAN---LARQDGSIHLN-YKDDTRITGATSDKGLV--------AIK 361  V+++ +  +     N    A+  G++ LN Y        AT  D G V        +I Sbjct: 454 TVRLNAENALSGGEYNGIFFAKNGGTLDLNGYNQSFNKIAAT--DSGAVITNTSTKKSIL 511 Query: 362 PLNNTNIVADTIHYKG-----DVLAVNKGKVELDFTPNILLAGRLDNFSGLT 408  LNNT   AD I++       DVL  ++ K E      ++L G +D  + ++ Sbjct: 512 SLNNT---ADYIYHGNINGNLDVLQHHETKKE---NRRLILDGGVDTTNDIS 557

The protein was expressed in E.coli as an insoluble 95.92 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 40

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 79> which encodes amino acid sequence <SEQ ID 80; NGS40>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.18    Possible cleavage site: 17 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.05 threshold:  0.0    PERIPHERAL Likelihood =  7.05   modified ALOM score:  −1.91 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.108(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 41

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 81> which encodes amino acid sequence <SEQ ID 82; NGS41>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    signal Score (−7.5): −2.47    Possible cleavage site: 17 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:  calculated from 16 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.37 threshold:  0.0    PERIPHERAL Likelihood =  7.37   modified ALOM score:  −1.97 Rule: inner or outer membrane protein Rule: inner or outer membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----     bacterial outer membrane --- Certainty= 0.790(Affirmative)     < succ>

The protein has no homology sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 42

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 83> which encodes amino acid sequence <SEQ ID 84; NGS42>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.2    Possible cleavage site: 14 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  6.58 threshold:  0.0    PERIPHERAL Likelihood =  6.58   modified ALOM score:  −1.82 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.514(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 43

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 85> which encodes amino acid sequence <SEQ ID 86; NGS43>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.34    Possible cleavage site: 39 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  2  value:  −4.78 threshold:  0.0    INTEGRAL  Likelihood =  −4.78  Transmembrane 1881-1897    (1876-1898)    INTEGRAL  Likelihood =  −1.01  Transmembrane 1966-1982    (1966-1982)    PERIPHERAL Likelihood =    1.91   modified ALOM score:  1.46 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.291(Affirmative)     < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 44

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 87> which encodes amino acid sequence <SEQ ID 88; NGS44>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.49    Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  1  value:  −1.33 threshold:  0.0    INTEGRAL  Likelihood =  −1.33  Transmembrane 141-157    (140-157)    PERIPHERAL Likelihood =    2.54   modified ALOM score:  0.77 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.153(Affirmative)     < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 45

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 89> which encodes amino acid sequence <SEQ ID 90; NGS45>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.07    Possible cleavage site: 46 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  2.07 threshold:  0.0    PERIPHERAL Likelihood =  2.07   modified ALOM score:  −0.91 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.333(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_049512.1|putative portal protein [Bacteriophage 933W] ref|NP_050550.1|hypothetical protein [Bacteriophage VT2-Sa] gb|AAD25457.1|AF125520_52 (AF125520) putative portal protein [Bacteriophage 933W] dbj|BAA84334.1|(AP000363) hypothetical protein [Bacteriophage VT2-Sa] dbj|BAA94158.1|(AP000422) portal protein [Escherichia coli] O157:H7] Length = 714 Score = 314 bits (805), Expect = 2e−84 Identities = 213/658 (32%), Positives = 327/658 (49%), Gaps = 22/658 (3%) Query: 7 ETGVLPDKNGEPLTIG---EYRLFVGEMMNQPAWRAVADKEMDYADGRQLDNELLQKQR 62 ET  +  KN    T      + +    ++ +QP WR  A+K   Y DG QL  E+LQ  + Sbjct: 4 ETNTMATKNDNGATPRFSQRQLQALCSDIDSQPKWRDAANKACAYYDGDQLPPEVLQVLK 63 Query: 63 ELGLPPAVENLITPTLLSVQGYEATIRTDWRVTADGETGGRD-VADALNFKLNRAERQSR 121 + G P  + NLI PT+  V G EA  RTD  V +D      + +A+A+N +   A R Sbjct: 64 DRGQPMTIHNLIAPTVDGVLGMAKTRTDLVVMSDEPDDETEKLAEAINAEFADACRLGN 123 Query: 122 ADKACSDAFRGQIACGIGWVTRNPNPFEFPYECGVIHRNAIHWDMKSYKYDLSDARWL 181  +KA SDA+  QI  G+ WVEV RN +PF   ++   + RN + WD  S + DLSD RWL Sbjct: 124 MNKARSDAYAEQIKAGLSWVEVRRNSDPFGPEFKVSTVSRNEVFWLSREADLSDCRWL 183 Query: 182 IRRWLLPERLAQFFPEYAGHFKAMGRGGSDWR-ISGELDGGGNTGLADAWGISGRNTV 240 +RRRW+  +     FP   G  + +     DWR      +  G  +L  AW Sbjct: 184 MRRRWMDTDEAKATFP---GMAQVIDYAIDDWRGFVDTTVTEOQPSPLMSAWEEYQSWDR 240 Query: 241 SEEFWFNETTRELAVAEVWYRRWVTADCLRDKKTGRTVEFDGANPNHREMAANGAV-LFA 299  +  W     R + +  V+YR +     + +   GR V FD  N       A+G V + Sbjct: 241 QQNEWLQRERRRVLLQVVYYRTFERLPVI-ELSNQRVVAFDKNNLMQAVAVASGRVQVKV 299 Query: 300 ASVPRMRRAFVVGDLVVRDEPTPYPHQKFPYPFFGFREDNTGIPYVRNMKYAQDNLN 359   V R+R A+ VG   + D P   P   FP VPF+G++R+D TG PYG +     AQD +N Sbjct: 300 GRVSRIREAWFVGPHFIVDRPCSAPQGMFPLVPFWGYRKDKTGEPYGLISEAIPAQDEVN 359 Query: 360 STNSKLRWGLSAIRTVRTKGIVDMSDEQFRRNIARVDADIVLNKIEAAQPGAR--FDVSR 417     KL W L A R +  +    +SD      I R D  I LN +   Q      F V + Sbjct: 360 FRRIKLTWLLQAKRVIMDEDATQLSDNDLMEQIERPDGIIKLNPVRKNQKSVADVFRVEQ 419 Query: 418 DFELSAQHWQMLQDSRATIRQISGITPSVGNRGNATSGRQESIQVEQSNQSLGLVMDNF 477 DF++++Q +Q++Q+S   I+   G+  +F+G    ATSG   S  VEQ   +L  + DN+ Sbjct: 420 DFQVASQQFQVMQESEKLIQDTMGVYSAFLGQDSGATSGVAISNLVEQGAPLAEINDNY 479 Query: 478 RQSRSLVGELLLAMIIEDLGS-DEQTVVIEGDAVTQGRTVVINRPETDPVTGKAYLSNDL 536 + +   VG LLLA +++DL       VVI  D   + +T+V+N  E D       L+ND+ Sbjct: 480 QFACQQVGRLLLAYLLDDLKKRRNHAVVINRDDRQRRQTIVLN-AEGD----NGELTNDI 534 Query: 537 QNIRLKVALEDVPSTNSYRSQQLGAMSEAVKSLPPEYQAAVLPFMVSLMDIPFKDKVIEK 596   +   +AL  V  T ++++Q    MSE ++ LPP+ QA VL   V+L+D+P K + +E+ Sbjct: 535 SRLNTHIALAPVQQTPAFKAQLAQHMSEVIQGLPPQVQAVVLDLWVNLLDVPQKQEFVER 594 Query: 597 IK-EVRVQETPEQI--EARIAQAVQDALAKSGNDIKRRELALKEQRTASEIKEIEARA 651 I+  +   ++P+++  E +   A Q AL +   +++ RE+A +  +  ++     A A Sbjct: 595 IRAALGTPKSPDEMTPEEQEVAAQQQALQQQQAELQMREMAGRVAKLEADAARAHAAA 652

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 46

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 91> which encodes amino acid sequence <SEQ ID 92; NGS46>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.25    Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  4.77 threshold:  0.0    PERIPHERAL Likelihood =  4.77   modified ALOM score:  −1.45 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.281(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >sp|P44184|YE10_HAEIN HYPOTHETICAL PROTEIN HI1410 pir||E64028 hypothetical protein HI1410-Haemophilus influenzae (strain Rd KW20) gb|AAC23058.1|(U32820) H. influenzae predicted coding region HI1410 [Haemophilus influenzae Rd] Length = 394 Score = 150 bits (379), Expect = 3e−35 Identities = 75/168 (44%), Positives = 114/168 (67%), Gaps = 2/168 (1%) Query: 57 REIQKSMRDSVHRLLKDIWAQLGLGHYEITDFEIRGANGTLFVFSGLQSHTVDSIKSFE 116 REIQKS+ DSV ++L D++  L L  F+++   +I G NG+ F F+GL+++ + SIKS Sbjct: 3 REIQKSISDSVIQMLADQIEMLSLQAFVQKTQIIGQNGSRFTFAGLKTN-ITSSIKSMT 61 Query: 117 GIDIVWVEEGHGVSKKSWDVLTPTIRKEGSEIWITLWPDMETDETYRRFIAMPSEDTWLC 176 GID+VWVEEG  VSK+SWD+L PTIR++GS+I ++NP    D+TY+RF+  P E Sbjct: 62 GIDVVWVEEGENVSESWDILIPTIREDGSQIIVSFNPKNILDDTYQRFVIHPPERCKSV 121 Query: 177 EINWRDNPWFPEALNRERLKAQRSMNKEDYGNIWEGRPRNVSEGAVYR 224  +NW+DNP+FP+L  E ++  R  + E Y +++EG P   S+ A+ + Sbjct: 122 LVNWQDNPYFPKEL-MEDMEQMRERDYELYRHVYEGEPVADSDLAIIK 168 >ref|NP_050979.1|P18 [Bacteriophage APSE-1] gb|AAF03961.1|AF157835_18 (AF157835) P18 [Bacteriophage APSE-1] Length = 469 Score = 117 bits (294), Expect = 2e−25 Identities = 72/233 (30%), Positives = 110/233 (46%), Gaps = 13/233 (5%) Query: 17 LFKPCRYKVMYXXXXXXXXXXXXXXXXXXXXQRPLRILCAREIQKSMRDSVHRLLKDKVA 76 +FKP R KV +                        R LC RE   S+ DS H +L+ +V Sbjct: 1 MFKPKRIKVYFGGRGGMKTVSFAKIALITASMHKRRFLCLREFMNSIEDSGHAVLQAEVE 60 Query: 77 QLGLGHFYEITDEEIRGANGTLFVFSGLQSHTVDSIKSFEGIDIVWVEEGHGVSKKSWDV 136  LGL + + I +  I G N ++F +  L +  + SIKS    D+ WVEE   VS+KS D Sbjct: 61 TLGLQNRFRILNTYIEGINDSIFKYGQL-ARNIASIKSKHDFDVAWVEEAETVSEKSLDS 119 Query: 137 LTPTIRKEGSEIWITLNPDMETDETYRRFIA-----------MPSEDTWLCEINWRDNPW 185 L PTIRK GSE+W + NP  E    Y+RF+               +D ++ ++++ DNPW Sbjct: 120 LIPTIRKPGSELWFSFNPAEEDGAVYKRFVKPYKELIDTQGYYEDDDLYVGKVSYLDNPW 179 Query: 186 FPEALNRERLKAQRSMNKEDYGNIWEGRPMVSEGAVYRHEIQDAFHSGRVTL 238  P  L  +  K +R  N + + +++ G      E A+ + E   +A     + L Sbjct: 180 LPAELKNDAQKMKRE-NYKKWRHVYGGECDANYEDALIQPEWVEAAIDAHIKL 231

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 47

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 93> which encodes amino acid sequence <SEQ ID 94; NGS47>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.87    Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  4.88 threshold:  0.0    PERIPHERAL Likelihood =  4.88   modified ALOM score:  −1.48 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.313(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_037739.1|Gp54 [Bacteriophage HK97] gb|AAF31132.1|(AF069529) Gp54 [Bacteriophage HK97] Length = 273 Score = 47.4 bits (111), Expect = 3e−04 Identities = 33/123 (26%), Positives = 52/123 (41%), Gaps = 20/123 (16%) Query: 242 NGGLSGKPKNANVPRRRKTHGVPLQEIADLYNEVLGGRLPSVQVLNDTRKRAIANRWCEM 301 NGG  G+ K    P RRK   +  +   + YN +G RLP    +N+ RKR +  + Sbjct: 160 NGGGDGQVK----PERRKAERIDYESFLNAYNTEVGDRLPHAVAVNEKRKRRL-KKIIPQ 214 Query: 302 LGTAAPNGKVRFGDKETGLAWFAGFFEKVA--MNPFHGENQTGPAVGFDWIFKAGNFVK 359 L T   +G             F  + R       PF+ G+N TG+   FD++ +  ++ Sbjct: 215 LKTPNVDG-------------FRAYVRAFHQAKPFFGDNDTGWTADFDYLLREDSLTG 261 Query: 360 ILE 362 + E Sbjct: 262 VRE 264

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 48

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 95> which encodes amino acid sequence <SEQ ID 96; NGS48>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.85    Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  7.16 threshold:  0.0    PERIPHERAL Likelihood =  7.16   modified ALOM score:  −1.93 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.379(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >dbj|BAA36059.1|(D90754) Outer membrane protein P.69 precursor [Escherichia coli] Length = 762 Score = 64.7 bits (156), Expect = 1e−09 Identities = 79/292 (27%), Positives = 121/292 (41%), Gaps = 55/292 (18%) Query: 3 NGARWTVTNDSMLKELDLSEDAQVEFSDNNK----FVKVSVSKLKGDGGVFKMYGDIV-- 56 N + W VT++S L  L LS    V+F+ +      F  ++V  L G+   F M  D+V Sbjct: 289 NNSVWNVTSNSNLDTLALSHST-VDFASHGSTAGTFATLNVENLSGNS-TFIMRADVVGE 346 Query: 57 ----KGESDKLITRKGSEGTHIIEYMDDAKAKTTGREYLKLVENKGNQEDNKASNKASYK 112       + D L     S G H++   +     TTG E L +V+      D  AS  AS + Sbjct: 347 GNGVNNKGDLLNISGSSAGNHVLAIRNQGSEATTGNEVLTVVKTT----DGAASFSASSQ 402 Query: 113 LNVRCTEQGGWCFALGESG------ASKKVNISTDGKRDF-------YLYPD-------- 151 +     E GG+ + + ++G      AS  V   T              + PD Sbjct: 403 V-----ELGGYLYDVRKNGTNWELYASGTVPEPTPNPEPTPAPAQPPIVNPDPTPEPAPT 457 Query: 152 ---TLTPGASSSVLFGEALYQLNAVSDETLVQRMGEIHADGMPQEDNNVWIKRVGGKFSG 208    T T  A  + L     Y LN V +TL+QRMG++       +D N+W++  GG Sbjct: 458 PKPTTTADAGGNYL--NVGYLLNYVENRTLMQRMGDLRNQ---SKDGNIWLRSYGGSLDS 512 Query: 209 SRSDYRVGGYGNRYWGFAGGFNRTGFGDKWIHYKGLMLRHLQSSYASEDYVG 260   S  ++ G+   Y G   G ++    D    Y GL   ++ S++AS DY G Sbjct: 513 FASG-KLSGFDMGYSGIQFGGDKR-LSDVMPLYVGL---YIGSTHASPDYSG 559

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 49

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 97> which encodes amino acid sequence <SEQ ID 98; NGS49>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −8.37    Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count:  0  value:  4.93 threshold:  0.0    PERIPHERAL Likelihood =  4.93   modified ALOM score:  −1.49 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.355(Affirmative)       < succ>     bacterial periplasmic space --- Certainty= 0.000(Not Clear)     < succ>      bacterial outer membrane --- Certainty= 0.000(Not Clear)      < succ>      bacterial inner membrane --- Certainty= 0.000(Not Clear)      < succ>

The protein has homology with the following sequences in the databases: gi|11282647|pir|H81959 patch repair protein (EC 3.1.-.-) NMA0429 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7379179|emb|CAB83728.1|(AL162753) patch repair protein [Neisseria meningitidis Z2491] Length = 140 Score = 256 bits (628), Expect = 8e−68 Identities = 131/140 (93%), Positives = 132/140 (93%) Query: 1 MTDIFTPSKRSFVMSKIHSKETKPEVLVRKFLFSQGFRYRKNDKRYAGKPDIVLPKYKTV 60 MTDIFT SKRSFVM KIHSKETKPEVLVRKFLF QGFRYRKNDKRY GKPDIVL KYKTV Sbjct: 1 MTDIFTTSKRSFVMLKIHSKETKPEVLVRFLFFQGFRYRKNDKRYVGKPDIVLSKYKTV 60 Query: 61 VFIHGCFWHGHSCNKGHIPKSNMDFWLEKITKNRERDIKNETELEKIGFKVIVVWECELK 120 VFIHGCFW+GHSCNKGHIPKSN DFWLEKITKN ERDIKNETELEKIGFKVIVVWECELK Sbjct: 61 VFIHGCFWYGHSCNKGHIPKSNTDFWLEKITKNCERDIKNETELEKIGFKVIVVWECELK 120 Query: 121 NKAICRERLNRLVEEIKDAV 140 NKAICRERLNRLV EIKDAV Sbjct: 121 NKAICRERLNRLVREIKDAV 140

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 50

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 99> which encodes amino acid sequence <SEQ ID 100; NGS50>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.6    Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.80 threshold: 0.0    PERIPHERAL Likelihood = 7.80    modified ALOM score:  −2.06 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.398(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11352963|pir||G81959 conserved hypothetical protein NMA0428 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7379178|emb|CAB83727.1|(AL162753) conserved hypothetical protein [Neisseria meningitidis Z2491] Length = 548 Score = 371 bits (954), Expect = e−102 Identities = 189/197 (95%), Positives = 194/197 (97%) Query: 1 VKGESGVDIENWKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW 60 VKGESGVDIE+WKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW Sbjct: 350 VKGESGVDIEDWKNKLPEKEREPVEVILNRLEDSELTNKEQAEVISALHSIIPEYPYYHW 409 Query: 61 RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEKAFGSKKS 120 RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIE+AFGSK S Sbjct: 410 RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEQAFGSKKS 469 Query: 121 MLLLTNNKTQAEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 180 +LLLTNNKT+AEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS Sbjct: 470 ILLLTNNKTKAEQNLEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 529 Query: 181 YLLRKVEQTKKRAKPTS 197 YLLRKVEQTKKR+K  S Sbjct: 530 YLLRKVEQTKKRSKVVS 546 >gi|10955124|ref|NP_059780.1|ymh [Agrobacterium tumefaciens] gi|5738274|gb|AAB91582.2|(AF242881) ymh [Agrobacterium tumefaciens] Length = 266 Score = 58.7 bits (141), Expect = 5e−08 Identities = 40/127 (31%), Positives = 69/127 (53%), Gaps = 5/127 (3%) Query: 61 RHLHQDLHTACNDFYNEKKDYLSAAIEAVKVFEDKVQKQTGLHSIDGRELIEKAFGSKKS 120 R +H D+   C +      +Y  A +EAVK   DK++++TGL + DG  L+++AF Sbjct: 137 RGVHPDVLRFCREEL-LVDNYFHAVLEAVKSVADKIRQTGL-TDDGAVLVDRAFSGDAP 194 Query: 121 MLLLTNNTQAEQNEDGLEQLACGTWTGFRNPVQHELRANLSPSIFNDKDALDLISLVS 180 ML +   ++++E+  + G   L  GT++ FRN   H  R +   S    +DA DL S+ S Sbjct: 195 MLAINELQSESEKGEQRGFSNLVKGTFSMFRNTTAHAPRIHWQMS---KEDAEDLFSMFS 251 Query: 181 YLLRKVE 187  + R+++ Sbjct: 252 LMHRRID 258

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS50 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 51

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 101> which encodes amino acid sequence <SEQ ID 102; NGS51>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.14    Possible cleavage site: 42 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.67 threshold: 0.0    PERIPHERAL Likelihood = 5.67    modified ALOM score:  −1.63 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.145(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||G81959 conserved hypothetical protein NMA0428 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB83727.1|(AL162753) conserved hypothetical protein [Neisseria meningitidis Z2491] Length = 548 Score = 532 bits (1371), Expect = e−150 Identities = 272/285 (95%), Positives = 280/285 (97%) Query: 1 MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60 MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK Sbjct: 1 MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60 Query: 61 DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALFRLGNKIEISTIQG 120 DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALF LGNKIEISTIQG Sbjct: 61 DNGIGMSFDEINDFYLRIGRNRREEKQASPCGRIPTGKKGLGKLALFRLGNKIEISTIQG 120 Query: 121 NERVTFTLDYAEIKKSERIYQPEFQKESVKPNTENGTTITLTELTKKQGYPLDNYVGHLS 180 NERVTFTLDYAEI++S+ IYQPEF+KESV+ N E+GTTITLTELTKKQGYPLDNYV HLS Sbjct: 121 NERVTFTIDYAEIRRSKGIYQPEFRKESVESNIESGTTITLTELTKKQGYPLDNYVEHLS 180 Query: 181 RLFDFPAQDFKIKVSLNGSEPRIIDGNLKYNLVTPQFEWEYQDLATNISSLSSKFEQYEY 240 RLFDFPAQDFKIKVSLNGSEP+IIDGNLKY+LVTPQFEWEYQDLATNISSLSSKFEQYEY Sbjct: 181 RLFDFPAQDFKIKVSLNGSEPKIIDGNLKYDLVTPQFEWEYQDLATNISSLSSKFEQYEY 240 Query: 241 SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF 285 SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF Sbjct: 241 SGLIQGKFITTEKPLKNNMKGITLFANGRMVNMPEFFTDSESSHF 285 >emb|CAC22276.1|(AJ302030) putative heat shock protein [Listeria monocytogenes] Length = 181 Score = 70.2 bits (171), Expect = 2e−11 Identities = 57/173 (32%), Positives = 90/173 (51%) , Gaps = 10/173 (5%) Query: 1 MSEEKLKMSFEPTVIEHLGVKMYSHTVPAIAELIANAYDACATEVEVRLFDKPEHKIVIK 60 MSE++  +  +P ++E LG  +Y++    + ELIANAYDA A  V V      E+K++++ Sbjct: 1 MSEKEYNLDIDPRILELLGPHLYTNIYYILGELIANAYDADAKNVYVIDRIDEENKLIVE 60 Query: 61 DNGIGMSFD--EINDFYLRIGRNRREEKQASPC---GRIPTGKKGLGKLALFRLGNKIEI 115 D+G GMS++  ++ +F L + +  R     S      R   G+KG+GKLA   +   + I Sbjct: 61 DDGSGMSYENKDVKNF-LSVAKESRTNAINSYTKLNNRRKMGRKGVGKLASLSVSENVNI 119 Query: 116 STIQGNERVFTLDYAEI-KKSERIYQPEFQKESVKPNTENGTTITLTELTKK 167  TI+  E+  F L    I KK E I +       +K    +GT I +T  T K Sbjct: 120 KTIKDGEKSGFVLSRKVINKKLEAINEDTISFIKIK---NHGTAIEMTNPTYK 169

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS51 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 52

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 103> which encodes amino acid sequence <SEQ ID 104; NGS52>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.5    Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.64 threshold: 0.0    PERIPHERAL Likelihood = 7.64    modified ALOM score:  −2.03 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.213(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: 2.1.1.73) NMA0427 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7379177|emb|CAB83726.1|(AL162753) modification methylase (cytosine- specific DNA methylase) [Neisseria meningitidis Z2491] Length = 351 Score = 310 bits (794), Expect = 8e−84 Identities = 152/154 (98%), Positives = 153/154 (98%) Query: 1 LGMENGFPKIMAGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI 60 LGMENGFPKI+AGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI Sbjct: 198 LGMENGFPKIIAGHQDETDFMHSCAGLSDINLKRLALIPKNGGNRLAFAHIPELQLECFI 257 Query: 61 GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRAFAHPEEDRALSLREGATLQSFPRNYVF 120 GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRAFAHPEEDRALSLREGATLQSFPRNYVF Sbjct: 258 GKDNSFKDTFGRLWWDKPAPTITTKFFSISNGRAFAHPEEDRALSLREGATLQSFPRNYVF 317 Query: 121 KAGSRDKIARLIGNAVPPMYTEKIGRAIVDNIEC 154 KAGSRDKIARLIGNAVPPMY EKIGRAIVDNIEC Sbjct: 318 KAGSRDKIARLIGNAVPPMYAEKIGRAIVDNIEC 351 >gi|1274411|sp|P25265|MTD2_HERAU MODIFICATION METHYLASE HGIDII (CYTOSINE-SPECIFIC METHYLTRANSFERASE HGIDII) (M.HGIDII) gi|538661|pir||JT0594 site-specific DNA-methyltransferase (cytosine-specific) (EC 2.1.1.73)-Herpetosiphon aurantiacus gi|487731|emb|CAA38941.1|(X55141) methyltransferase [Herpetosiphon aurantiacus] Length = 354 Score = 95.6 bits (237), Expect = 3e−19 Identities = 62/142 (43%), Positives = 82/142 (57%), Gaps = 9/142 (6%) Query: 12 AGHQDETDFM HSCAGLSDINLKRLALIPKNGGNRLAFAHIP-ELQLECFIGKD-NSFKDT 69 +G   E D MH+ + L DINL+R+      G     +A  P EL  EC   +   S+ Sbjct: 200 SGGHWEGDSMHAASRLEDINLRRIQHSVPGG----TWADWPEELIAECHKKESGESYGSV 255 Query: 70 FGRLWWDKPAPTITTKFFSISNGEFAHPEEDRALSLREGATLQSFPRNYVFKAGSRDK-- 127 +GR+ WDK APTITT+     NGRF HPE+DRA+SLRE A LQ+FPR+Y F    + K Sbjct: 256 YGRMEWDKVAPTITTQCNGYGNGRFGHPEQDRAISLRALLQTFPRSYQFAPEGQLKFK 315 Query: 128 -IARLIGNAVPPMYTEKIGRAI 148  ++R IGNAVP      I ++I Sbjct: 316 TVSRQIGNAVPVALGRVIAKSI 337

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS52 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 53

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 105> which encodes amino acid sequence <SEQ ID 106; NGS53>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −7.56    Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.36 threshold: 0.0    PERIPHERAL Likelihood = 5.36    modified ALOM score:  −1.57 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.189(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11256915|pir||F81959 site-specific DNA-methyltransferase (cytosine- specific) (EC2.1.1.73) NMA0427 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7379177|emb|CAB83726.1|(AL162753) modification methylase (cytosine- specific DNA methylase) [Neisseria meningitidis Z2491] Length = 351 Score = 247 bits (606), Expect = 5e−65 Identities = 124/149 (83%), Positives = 127/149 (85%) Query: 1 LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG 60 LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG Sbjct: 59 LQPETLEKELGLKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPG 118 Query: 61 YVVVENVPGILSRMKESGLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT 120 YVVVENVPGILSRMKESGLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT Sbjct: 119 YVVVENVPGILSRMKESGLDNFIKLLEEKGFTVHFGIHNTADYGIPQSRKRFTLIANRIT 178 Query: 121 KKSWNQSSIRANGLRYAMFWEWKTAFPKL 149 K+           L        +  FPK+ Sbjct: 179 KEKLEPVKYSGKRLTVRDVLGMENGFPKI 207 >gi|127441|sp|P25265|MTD2_HERAU MODIFICATION METHYLASE HGIDII (CYTOSINE- SPECIFIC METHYLTRANSFERASE HGIDII) (M.HGIDII) gi|538661|pir||JT0594 site-specific DNA-methyltransferase (cytosine- specific) (EC 2.1.1.73)-Herpetosiphon aurantiacus gi|48773|emb|CAA38941.1|(X55141) methyltransferase [Herpetosiphon aurantiacus] Length = 354 Score = 71.9 bits (169), Expect = 4e−12 Identities = 39/105 (37%), Positives = 57/105 (54%), Gaps = 1/105 (0%) Query: 12 LKKNDDDLILIGCSPCQYWSVIQTDKRKSEKSKSLLLEFQRFVEYFNPGYVVVENVPGIL 71 L  N+IL+GC+PCQ +S   T K ++     LL EF R +    P  + +ENVP + Sbjct: 64 LYPNNQHKILVGCAPCQDFSQY-TKKSRTGTKWQLLTEFSRLIREIEPDIISMENVPEVR 122 Query: 72 SRMKESGLDNFIKLLEEKGFTHFGIHNTADYGIPQSSRKRFTLIA 116 +  +    +NFI+ LE+ G+ V   + +  DYGIPQ R R  L A Sbjct: 123 TFNRGEVFNFIQSLEQLGYWSHSVVHCPDYGIPQQRDRLVLFA 167

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS53 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 54

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 107> which encodes amino acid sequence <SEQ ID 108; NGS54>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.82    Possible cleavage site: 50 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.89 threshold: 0.0    PERIPHERAL Likelihood = 6.89    modified ALOM score:  −1.88 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.253(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: gi|1074456|pir||D64155 hypothetical protein HI0597-Haemophilus influenzae (strain Rd KW20) gi|1573586|gb|AAC22254.1|(U32741) conserved hypothetical protein [Haemophilus influenzae Rd] Length = 272 Score = 188 bits (459), Expect = 2e−47 Identities = 95/100 (95%), Positives = 97/100 (97%) Query: 1 MNLPFRAMVSDLGGTLLTPEHLVGDLTIDTLRVLEQKGVDIILATGRNHTDMSSILGKIG 60 MNLPFRAMVSDL GTLLTPEHLVGDLTIDTLR LEQKGVDIILATGRNHTD+SSILGKIG Sbjct: 1 MNLPFRAMVSDLDGTLLTPEHLVGDLTIDTLRALEQKGVDIILATGRNHTDVSSILGKIG 60 Query: 61 AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKTSY 100 AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKT + Sbjct: 61 AERAVMITSNGARVRDLQGNLLYSNSLPEELVLELYKTPF 100

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS54 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 55

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 109> which encodes amino acid sequence <SEQ ID 110; NGS55>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.46    Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.02 threshold: 0.0    PERIPHERAL Likelihood = 3.02    modified ALOM score:  −1.10 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.311(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: aeruginosa (strain PAO1) gi|9948791|gb|AAG06104.1|AEOO4699_9 (AE004699) probable FMN oxidoreductase [Pseudomonas aeruginosa] Length = 411 Score = 279 bits (686), Expect = 2e−74 Identities = 157/375 (41%), Positives 228/375 (59%), Gaps 10/375 (2%) Query: 1 MEEQLAQNDQ-PSEKLVRLYGAWAEGGAGVLVTGNVMVAESGKGSINDVLISDDRALKLM 59 MEE +4   Q PSE4+L+RLY AWA+GGAG+L++GNVMV          V++ DD  LE Sbjct: 24 MEENMADAAQAPSERLMRLYQAWADGGAGLLISGNVMVDSRAMTGPGGVVLEDDAQLEKF 83 Query: 60 KKWAKARTQNDTLLIMQINKAGKQSPAVKTPLAPSAVPL--GMNGFINPPRELSADE 117 ++WA+          +QINH G+Q  A + +   APSAVPL   GM+     P+ + Sbjct: 84 RRWARIGRSAGAGFWLGINHPGRQMQANLGQQAWAPSAVPLELGGMSRHFATPKAMDEAM 143 Query: 118 INGLIQQFVQTAKIAEQAGFSGVQIYAVHGYLISQFLSPHHNRRQDQWGGSLENRMRFLL 177 I  +IQ+F ++ +AE+AGFSGV+I+A HGYL+SQFLSP  NRR D WGGSLENR R LL Sbjct: 144 IAEVIQRFARSAGLAERAGFSGVEIHHGYLLSQFLSPLSNRRSDAWGGSLENRARLLL 203 Query: 178 ETYTAIRAAGKDFLVGVXLNSADFQKGGFDESESVQVVQKLSEMGIDFIEVSGGNYESP 237 E   A+RA     F V VKLNSADFQ+GGF   ++ +VV+ L  +G+D +E+SGG+YE+P Sbjct: 204 EIVRAVRAEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAP 263 Query: 238 QMLA-AKDS-TRKREAFFIDYAEKARAASQAPLIITGGFRSQTAMEDALSSGHLDLVGIA 295  M   A+D  T  REA+F+++A   RAA++ P+++TGG R +   E  L+SG +D+VGI Sbjct: 264 AMQGEARDGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRVAEQVLASG-VDMVGIG 322 Query: 296 RPFALVPDLANKMQNRTYQTVQADRIQTGVDKKAGAMLEMNWYMTQMDLIGQGKQSN 355    A+ P+L    +       Q   I     + +K   ++  M     Q+  + +G+ +N Sbject: 323 TALAIEPNLPRDWRAGKDSAPQLRPI----TWENKPLASLANMAVKFQLRKLSRGRATN 378 Query: 356 PKIVGVESIAENFAG 370 P++  ++    AG Sbjct: 379 PRVSPLCALLAQQAG 393

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 56

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 111> which encodes amino acid sequence <SEQ ID 112; NGS56>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.69    Possible cleavage site: 54 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.29 threshold: 0.0    PERIPHERAL Likelihood = 4.29    modified ALOM score:  −1.36 *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.042(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|7444004|pir||D70029 transcription regulator ArsR family homolog yvbA- Bacillus subtilis gi|2635892|emb|CAB15384.1|(Z99121) similar to transcriptional regulator (ArsR family) [Bacillus subtilis] Length = 90 Score = 51.3 bits (118), Expect = 3e−06 Identities = 24/65 (36%), Positives = 42/65 (63%), Gaps = 1/65 (1%) Query: 15 IFTVLSDENRHQILHVLWKHGRMNVNELTEHLHLSRPAVSHHLKIMLQAGAVAVEQVGKE 74 +F  +SD  R +IL +L K G M   ++ EH ++S+P++SHHL I+QA  ++  + G+ Sbjct: 4 VFKAISDPTRRKILDLL-KGGDMTAGDIAEHFNISHPSISHHLNILKQAEVISDHRKGQF 62 Query: 75 RFYSI 79  +YS+ Sbjct: 63 IYYSL 67

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 57

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 113> which encodes amino acid sequence <SEQ ID 114; NGS57>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −2.57    Possible cleavage site: 55 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.67 threshold: 0.0    PERIPHERAL Likelihood = 5.67    modified ALOM score:  −1.63 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.160(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|10444407|gb|AAG17897.1|AF297971_1 (AF297971) restriction endonuclease R.NgoMIII [Neisseria gonorrhoeae] Length = 213 Score = 319 bits (818), Expect = 1e−86 Identities = 156/156 (100%), Positives = 156/156 (100%) Query: 1 LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL 60 LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL Sbjct: 58 LYKQYADWNRLSYNAPIYVGKAVPKGWRQARNSDNALNQSTELFHRLKEHSRSIAAVSDL 117 Query: 61 DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCDGFGNHDPGKGRYEQAKSDWD 120 DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCDGFGNHDPGKGRYEQAKSDWD Sbjct: 118 DPSDFMCRFVIFEGAGSDMIGTIEAALIKLHKPLWNSCDGFGNHDPGKGRYEQAKSDWD 177 Query: 121 VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK 156 VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK Sbjct: 178 VLHSGRVWADRLNGIPNSYESILENINTHLEIIKRK 213

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 58

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 115> which encodes amino acid sequence <SEQ ID 116; NGS58>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −1.92    Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.41 threshold: 0.0    PERIPHERAL Likelihood = 5.41    modified ALOM score:  −1.58 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.107(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|10444408|gb|AAG17898.1|AF29797_2 (AF297971) DNA cytosine methyltransferase M.NgoMIII [Neisseria gonorrhoeae] Length = 377 Score = 759 bits (1960), Expect = 0.0 Identities = 377/377 (100%), Positives = 377/377 (100%) Query: 1 MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ 60 MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ Sbjct: 1 MKSLEIFSGAGGLAKGLELAGFQHASFIELNKDACNSLRSNFNPKLVYQGDVADFDLSSQ 60 Query: 61 EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA 120 EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA Sbjct: 61 EGIEVIAGGPPCQPFSLGGKHLAHEDRRDMFPHAVRYVEYYRPKAFIFENVKGLLRKSFA 120 Query: 121 DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK 180 DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK Sbjct: 121 DYFEYILLRLTYPNLGILQNEDWKGHLTRLKEIEFNLYKGIKYKVSYQLLNAADYGVPQK 180 Query: 181 RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK 240 RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK Sbjct: 181 RERVVIVGIRADLDIDWKFPKRTHSEDRLNWEKYVTGEYWEKHNEPKRFNKDIAEKLQKK 240 Query: 241 YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG 300 YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG Sbjct: 241 YGIFEPEKKPWQTVRDTLSDIPHPLGNHKITGHEYRDGARIYPGHTGSGIDEPSKTIKAG 300 Query: 301 GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI 360 GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI Sbjct: 301 GHGVPGGENMIRYDDGTVRYFTSYEAKLLQTFPEEFVISGAWGEAMRQIGNAVPVKLSEI 360 Query: 361 LGKHLMGVLSEKSSLHN 377 LGKHLMGVLSEKSSLHN Sbjct: 361 LGKHLMGVLSEKSSLHN 377

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 59

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 117> which encodes amino acid sequence <SEQ ID 118; NGS59>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.82    Possible cleavage site: 60 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.86 threshold: 0.0    PERIPHERAL Likelihood = 2.86    modified ALOM score:  −1.07 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.197(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11353338|pir||F81882 hypothetical protein NMA1155 [imported] Neisseria meningitidis (group A strain Z2491) gi|7379848|emb|CABB4417.1|(AL162755) hypothetical protein NMA1155 [Neisseria meningitidis Z2491] Length = 120 Score = 131 bits (329), Expect = 2e−30 Identities = 64/68 (94%), Positives = 67/68 (98%) Query: 1 LSDISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS 60 +S+ISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS Sbjct: 1 MSNISASRAAYMDVQKQYPFETVAVCVLPNHIHAIWTLPPDDADYSLLRRLIKTKFSAYS 60 Query: 61 PHTKNLGA 68 P+TKNL A Sbjct: 61 PYTKNLSA 68

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 60

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 119> which encodes amino acid sequence <SEQ ID 120; NGS60>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.14    Possible cleavage site: 16 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.76 threshold: 0.0    PERIPHERAL Likelihood = 2.76    modified ALOM score:  −1.05 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.330(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11281269|pir||D81804 hypothetical protein NMA1789 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7380430|emb|CAB85016.1|(AL162757) hypothetical protein [Neisseria meningitidis Z2491] Length = 243 Score = 154 bits (389), Expect 5e−37 Identities = 82/85 (96%), Positives = 82/85 (96%) Query: 12 MNTKTELQKLLEEDISTLKETLIRVDALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT 71 MNTKTELQKLLEEDISTL ETLI  DALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT Sbjct: 1 MNTKTELQKLLEEDISTLTETLICADALPPRYVRSIATPIVRRWLIDKQLNILAKEIGLT 60 Query: 72 IELPILDTSLVFEKLSTLENKVNFY 96 IELPILDTSLVFEKLSTLENKVNFY Sbjct: 61 IELPILDTSLVFEKLSTLENKVNFY 85

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS60 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 61

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 121> which encodes amino acid sequence <SEQ ID 122; NGS61>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.88    Possible cleavage site: 32 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.52 threshold: 0.0    PERIPHERAL Likelihood = 5.52    modified ALOM score:  −1.60 Rule: cytoplasmic protein *** Reasoning step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.300(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11281269|pir||D81804 hypothetical protein NMA1789 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7380430|emb|CAB5016.1|(AL162757) hypothetical protein [Neisseria meningitidis Z2491] Length = 243 Score = 193 bits (491), Expect = 5e−49 Identities = 96/101 (95%), Positives = 97/101 (95%) Query: 1 MAGGVYLGGKIISPIYHSSQEFSGEPIIYAETNIILCPAEKFLTLKRVFHNGNIFNMNQI 60 MAGGVYLGG+ IS IYHSSQEFSGEPIIYAETNIILCPAEKFLTLKRVFHNGNIFNMNQI Sbjct: 86 MAGGVYLGGEFISSIYHSSQEFSGEPIIYAEPNIILCPAEKFLTLKRVFHNGNIFNMNQI 145 Query: 61 ITFLSNKQGGVRFDKNYDKYKTWQVAIEKAANFLKLGNPYN 101 ITFLSNKQGGV FDKNYDKYKTWQVAIEKAANFLKLGNPYN Sbjct: 146 ITFLSNKQGGVHFDKNYDKYKTWQVAIEKAANFLKLGNPYN 186)

As a homolog (amino acids 1-96) was found in serogroup A N.meningitidis but not in serogroup B, NGS61 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 62

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 123> which encodes amino acid sequence <SEQ ID 124; NGS62>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −2.43    Possible cleavage site: 44 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.72 threshold: 0.0    PERIPHERAL Likelihood = 4.72    modified ALOM score:  −1.44 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.324(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

A homolog was found in serogroup A N.meninigitidis but not in serogroup B, so NGS62 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 63

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 125> which encodes amino acid sequence <SEQ ID 126; NGS63>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.74    Possible cleavage site: 24 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of predicted Mature Form:   calculated from 25 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 10.72 threshold: 0.0    PERIPHERAL Likelihood = 10.72    modified ALOM score:  −2.64 Score for OM-PP discrimination: −22.14 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −22.14 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 2.21378 Periplasmic space? Score: 2.21378 ----- Final Results -----     bacterial periplasmic space --- Certainty=     0.931(Affirmative) < succ>     bacterial outer membrane --- Certainty=     0.237(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11284146|pir||B81142 hypothetical protein NMB0912 [imported]-Neisseria meningitidis (group B strain MD5B) gi|7226150|gb|AAF41320.1|(AE002443) hypothetical protein [Neisseria meningitidis MC58] Length = 208 Score = 51.7 bits (119), expect = 3e−06 Identities = 30/72 (41%), Positives = 40/72 (54%) Query: 5 LLKNWKPLLILSAIAFFAVSWQLDRAAQYRRGYGAAVSEVSERLKAAAVEHAEHARKSSA 64 LLK WKP+ +L  I     +W  DRA +YR G  AA +E+S RLK   +E A+ AR + Sbjct: 43 LLKYWKPVGVLLLIVLIFTAWHFDRAEKYRMGREAAAAEISNRLKDGYIEQAKQARSAEQ 102 Query: 65 AYQAQKAAEEEK 76    A  A R+ K Sbjct: 103 KAAAAPAERQTK 114

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 64

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 127> which encodes amino acid sequence <SEQ ID 128; NGS64>. Analysis of this protein sequence reveals the following: McG: Examining signal sequence (McGeoch)    Length of UR: 0    Peak Value of UR: 2.99    Net Charge of CR: 4    Discriminant Score: 5.35 GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −2.53    Possible cleavage site: 33 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.23 threshold: 0.0    PERIPHERAL Likelihood = 3.23    modified ALOM score:  −1.15 *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.054(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 65

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 129> which encodes amino acid sequence <SEQ ID 130; NGS65>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.61    Possible cleavage site: 61 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.34 threshold: 0.0    PERIPHERAL Likelihood = 3.34    modified ALOM score:  −1.17 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.236(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|1175791|sp|P44189|YE18_HAEIN HYPOTHETICAL PROTEIN HI1418 gi|1074769|pir||A64029 hypothetica1 protein HI1418-Haemophilus influenzae (strain Rd KW20) gi|1574254|gb|AAC23068.1|(U32821) H. influenzae predicted coding region HI1418 [Haemophilus influenzae Rd] Length = 201 Score = 104 bits (251), Expect = 1e−21 Identities = 58/119 (48%), Positives = 72/119 (59%), Gaps = 4/119 (3%) Query: 51 LKMQNTISFSFKSQNRTQI-LGAEPFCLGDVAEILQIQNAR---QLPLKDQGIQKSS 106 +K Q   S F+FK   VR  +    E WFC  DV  IL   N+R   Q   K  G+ K Sbjct: 14 MKNQIQFSTFFKDLPVRTILDPKGEFFCGTDVCHILGYTNSRKALQDHCKQGGVTKRY 73 Query: 107 VATKKGNQELLFINEPNLYRVIFRSRKAEAVFQDWIFEEVIPQIRKTGGYQITPKTTA 165   TK  +QE+ FINEPNLYR+I +SRK EA  F+ W+FEEV+PQIRKTG YQ+ P+  A Sbjct: 74 TPTKSADQEMTFINEPNLYRLIIKSRKPEAEPFEAWVFEEVLPQIRKTGKYQLQPQQLA 132 >gi|11281012|pir||A81144 hypothetical protein NMB0900 [imported]-Neisseria meningitidis (group B strain MD58) gi|7226137|gb|AAF41308.1|(AE002442) hypothetical protein [Neisseria meningitidis MC58] Length = 305 Score = 104 bits (249), Expect = 2e−21 Identities = 73/137 (53%), Positives = 93/137 (67%), Gaps = 2/137 (1%) Query: 190 YSMIHQRFNVEAVEGIPADKLPEAVAYHALTLHTG-LAGEVPDREPLPAPQPALPISGN 248 +S +  +F     E +PA++ PE ++ +  + +  G L GEV DREPLPAPQPALPISGN Sbjct: 164 WSAVKSKFGCSYKE-VPAEQFPELSMGRVAVENGVLYGEVLDREPLPAPQPALPISGN 222 Query: 249 ALADIAAMVYYGTRHIELGKDVSAPLKQLGCKQAVTMWTVWHETRSILKRSVAALEVLRG 308 AL D+A  V YG   I++G+DVS PLKQLGCRQAVTMWTVW ETRS LK +  ALE L Sbjct: 223 ALYDLAVAVRYGAWAIQMGRDVSLPLKQLGCKQAVTMWTVWAETRSRLKAAANALEALNA 282 Query: 309 YADKDASGRIAACLEGI 325 +AD + + +I   L  I Sbjct: 283 HADAEHAAKIRPMLPEI 299 >gi|7460273|pir||T13267 hypothetical protein-Lactococcus lactis phage BK5-T gi|928839|gb|AAA98590.1|(L44593) ORF266; putative [Lactococcus phage BK5-T] Length = 266 Score = 75.9 bits (179), Expect = 6e−13 Identities = 42/111 (37%), Positives = 63/111 (55%), Gaps = 3/111 (2%) Query: 55 NTISVFSFKSQNVRTQILGAEPWFCLGDVAEILQIQNAR---QLPLKDQGIQKSSVATKK 111 N +  F+F +  VRT ++  EPWF   DVA  +  +N R   +  +KD+  ++S + T Sbjct: 2 NELQNFNFNNLPVRTVLINDEPWFVGKDVAIAIGYKNFRDALKSHVKDKYKRESRITTPS 61 Query: 112 GNQELLFINEPNLYRVIFRSRKAEAVKFQDWIFEBVIPQIRKTGGYQITPK 162 G Q +  I+EP LY++   S+   A  FQDW++EEV+P IRK G Y    K Sbjct: 62 GVQSVTVISEPGLYQLAGESKLPSAEPFQDWEELPTIRKHGAYMTDAK 112

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 66

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 131> which encodes amino acid sequence <SEQ ID 132; NGS66>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.12    Possible cleavage site: 53 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 8.96 threshold: 0.0    PERIPHERAL Likelihood = 8.96    modified ALOM score:  −2.29 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.402(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 67

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 133> which encodes amino acid sequence <SEQ ID 134; NGS67>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): 5.71    Possible cleavage site: 22 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 23 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.81 threshold: 0.0    PERIPHERAL Likelihood = 2.81    modified ALOM score:  −1.06 Score for OM-PP discrimination: −32.34 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −32.34 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 3.23391 Periplasmic space? Score: 3.23391 ----- Final Results -----     bacterial periplasmic space --- Certainty=     0.928(Affirmative) < succ>     bacterial outer membrane --- Certainty=     0.199(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|7475078|pir||H69834 hypothetical protein yhjQ-Bacillus subtilis gi|2226189|emb|CAA74479.1|(Y14081) hypothetical protein [Bacillus subtilis] gi|2633396|emb|CAB12900.1|(Z99109) yhjQ [Bacillus subtilis] Length = 108 Score = 32.9 bits (74), Expect = 2.1 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 4/98 (4%) Query: 54 CLDAGQVCLTHCLSLLTQGDTSMSDCAVAVRQMLALCGAVHDLAAQNSPLTRDAAKVCLE 113 C+ A   C T CL    Q    +S C    R+   +C         +SP  ++   +C+ Sbjct: 15 CMKACNHCFTKCLEESVQ--HHLSGCIRLDRECADICALAVKAMQTDSPFMKEICALCAD 72 Query: 114 ACKQCAKACKEHSAHHAECKACYESCLDCIKECEKLAA 151  C+ C   C +H   H  C+AC ++C  C ++C  +AA Sbjct: 73 ICEACGTECGKHD--HDHCQACAKACFTCAEQCRSMAA 108 >gi|7479923|pir||T36241 hypothetical protein SCE39.31c-Streptomyces coelicolor gi|4582392|emb|CAB40339.1|(AL049573) hypothetical protein [Streptomyces coelicolor A3(2)] Length = 136 Score = 30.9 bits (69), Expect = 7.7 Identities = 27/102 (26%), Positives = 43/102 (41%), Gaps = 6/102 (5%) Query: 54 CLDAGQVCLTHCLSLLTQGDTSMSDCAVAVRQMLALCGAVHDLAAQ----NSPLTRDAAK 109 C  A   C   CLS  T  D  ++C         +C A   + ++    ++ +TR   + Sbjct: 34 CAQACTACADACLSEPTVAD--LTKCIRTDMDCADVCTATAAVLSRHTGYDANVTRAVLQ 91 Query: 110 VCLEACKQCAKACKEHSAHHAECKACYESCLDCIKECEKLAA 151  C   C  C   C  H+  H  C+ C E+C  C + C++L A Sbjct: 92 ACATVCAACGDECARHAGMHEHCRVCAEACRSCEQACQELLA 133

The protein was expressed in E.coli as a soluble 14.19 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 68

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 135> which encodes amino acid sequence <SEQ ID 136; NGS68>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.05    Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.25 threshold: 0.0    PERIPHERAL Likelihood = 5.25    modified ALOM score:  −1.55 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.220(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11353493|pir||A81795 hypothetical protein NMA2214 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7380833|emb|CAB85425.1|(AL162758) hypothetical protein [Neisseria meningitidis Z2491] Length = 208 Score = 263 bits (673), Expect = 3e−69 Identities = 140/145 (96%), Positives = 143/145 (98%) Query: 1 LDWRGNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPLCGEDTQR 60 LDWRGNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPL GEDTQR Sbjct: 44 LDWQGNKPLGAAELADLKPLYKDFMYWERGLHMYKASAVVPTGYVRVGNTAPLVGEDTQR 103 Query 63 YASFWGDGYDVYRQLRWRQIPEKQRKAFKKAAKSKNTVMFAGREYGISKQNLSDVWDDFE 120 YASFWGDGYDVYRQLRW+QIPEKQRKAFKKAAKSK TVMFAGREYGISKQNLSDVWDDFE Sbjct: 104 YASFWGDGYDVYRQLRWQQIPEKQRKAFKKAAKSKKTVMFAGREYGISKQNLSDVWDDFE 163 Query: 121 DAMELAKAFPCLSSLFLTKWHKNLYE 145 DAMELAKAFPCLSSLFLTKWHKNLY+ Sbjct: 164 DAMELAKAFPCLSSLFLTKWHKNLYD 188 >gi|11280955|pir|B81219 hypothetical protein NMB0273 [imported]-Neisseria meningitidis (group B strain MD58) gi|7225497|gb|AAF40727.1|(AE002383) hypothetical protein [Neisseria meningitidis MC58] Length = 141 Score = 216 bits (550), Expect = 5e−55 Identities = 117/121 (96%), Positives = 119/121 (97%) Query: 25 MYWERGLHMYKASAVVPTGYVRVGNTAPLCGEDTQRYASFWGDGYDVYRQLRWRQIPEKQ 84 MYWERGLHMYKASAVVPTGYVRVGNTAP CGEDTQRYASFWGDGYDVYRQLRW+QIPEKQ Sbjct: 1 MYWERGLHMYKASAVVPTGYVRVGNTAPLVGEDTQRYASFWGDGYDVYRQLRWQQIPEKQ 60 Query: 85 RKAFKKAAKSKNTVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY 144 RKAFKKAAKSK TVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY Sbjct: 61 RKAFKKAAKSKKTVMFAGREYGISKQNLSDVWDDFEDAMELKAFPCLSSLFLTKWHKNLY 120 Query: 145 E 145 + Sbjct: 121 D 121

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 69

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 137> which encodes amino acid sequence <SEQ ID 138; NGS69>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.63    Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.84 threshold: 0.0    PERIPHERAL Likelihood = 6.84    modified ALOM score:  −1.87 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty=       0.361(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|7464552|pir||C64707 hypothetical protein HP1499-Helicobacter pylori (strain 26695) gi|2314683|gb|AAD08545.1|(AE000648) H. pylori predicted coding region HP1499 [Helicobacter pylori 26695] Length = 272 Score = 38.2 bits (88), Expect = 0.13 Identities = 34/123 (27%), Positives = 58/123 (46%), Gaps = 10/123 (8%) Query: 3 EFKPIFGQDFGLSKKEAIRKVLKWLPSHLKFTLMVAQGIQG------FHPKAVFWKNDKN 56 EF+ I G DF  +  ++IR +L    ++ K         +       FHPK   + N K Sbjct: 54 EFEIIVGLDFKTTDSKSIRFLLDLNKTYKKLRFYCYGDKENNKTDIVFHPKIYMFDNGK- 112 Query: 57 EYYALIGSSNLTHAAFNSNYEAN-ILTKISEQDFIKVKSWADEI--AMKSIPVSEDWLEE 113 E  ++IGS+NLT     +N+E N I T+     + ++ +  + I  A      +E++L+ Sbjct: 113 EKTSIIGSTNLTKGGLENNFEVNTIFTEKKPLYYTQLNAIYNSIKYADSLFTPNEEYLQN 172 Query: 114 YQE 116 Y E Sbjct: 173 YNE 175

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS69 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 70

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 139> which encodes amino acid sequence <SEQ ID 140; NGS70>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −1.18    Possible cleavage site: 22 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 23 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.19 threshold: 0.0    PERIPHERAL Likelihood = 4.19    modified ALOM score:  −1.34 Score for OM-PP discrimination: −5.89 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −5.89 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 0.588927 Periplasmic space? Score: 0.588927 ----- Final Results -----     bacterial periplasmic space --- Certainty=     0.849(Affirmative) < succ>     bacterial outer membrane --- Certainty=     0.106(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11353344|pir||A81886 hypothetical protein NMAl183 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7379875|emb|CAB84445.1|(AL162755) hypothetical protein NMA1183 [Neisseria meningitidis Z2491] Length = 74 Score = 58.7 bits (141), Expect = 2e−08 Identities = 30/43 (69%), Positives = 32/43 (73%) Query: 62 IGGFGGVGGFGGLKPALVYRNFRIIATNRPAATRARPRQTTVA 104 +G|||G+|G|GGLKP|LVY|N||IIATNRPAATRA|PR|TTVA Sbjct: 32 MGNIDGIDGSGGLKPTLVYWNHCIIATNRPAATRAHPRHTTVA 74

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 71

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 141> which encodes amino acid sequence <SEQ ID 142; NGS71>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −1.98    Possible cleavage site: 28 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 29 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.04 threshold: 0.0    PERIPHERAL Likelihood = 5.04    modified ALOM score:  −1.51 Score for OM-PP discrimination: −9.17 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −9.17 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 0.916744 Periplasmic space? Score: 0.916744 ----- Final Results -----     bacterial periplasmic space --- Certainty=     0.923(Affirmative) < succ>     bacterial outer membrane --- Certainty=     0.146(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 72

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 143> which encodes amino acid sequence <SEQ ID 144; NGS72>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −3.18    Possible cleavage site: 42 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 4 value: −8.76 threshold: 0.0    INTEGRAL Likelihood = −8.76 Transmembrane    11-27 (8-37)    INTEGRAL Likelihood = −6.90 Transmembrane    80-96 (75-102)    INTEGRAL Likelihood = −2.39 Transmembrane    98-114 (98-114)    INTEGRAL Likelihood = −1.12 Transmembrane    47-63 (47-64)    PERIPHERAL Likelihood = 3.55    modified ALOM score:  2.25 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.450(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11354095|pir||H81995 probable transmembrane transport protein NMA0047 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7378822|emb|CAB83364.1|(AL162752) putative transmembrane transport protein [Neisseria meningitidis Z2491] Length = 405 Score = 257 bits (658), Expect = 5e−68 Identities = 152/162 (93%), Positives = 154/162 (94%) Query: 1 MTHTASKTPKLWAVIAAAAFILLITIGMRMTLGLFVQPVVNTTELNIAQFSLIITVFQLM 60 MTHTASKTPK W  I AAAFILLITIGMRMTLGLFVQPVVNTTEL+IAQFSLII VFQLM Sbjct: 1 MTHTASKTPKFWLTITAAAFILLITIGMRMTLGLFVQPVVNTTELNIAQFSLIITVFQLM 60 Query: 61 WGVLQPLSGALADRFGAFRVLSGGALLLVCACLIASNIPTYWGLMIAVGLLLAFGTGSGG 120 WGV QPLSGALADRFGAFRVLSGGA+LLVCACLIA NIPTYWGLMIAVGLLLAFGTGSGG Sbjct: 61 WGVSQPLSGALADRFGAFRVLSGGAVLLVCACLIAPNIPTYWGLMIAVGLLLAFGTGSGG 120 Query: 121 FSIIMGQVAAQVPTHKRGLASGLVNAGGSAGQFLFAPLVQGL 162 FSIIMGQVAAQVP HKRGLASGLVNAGGSAGQFLFAPLVQGL Sbjct: 121 FSIIMGQVAAQVPAHKRGLASGLVNAGGSAGQFLFAPLVQGL 162 >gi|11351469|pir||F83484 probable MFS transporter PA1286 [imported]- Pseudomonas aeruginosa (strain PAO1) gi|9947221|gb|AAG04675.1|AE004558_4 (AE004558) probable MFS transporter [Pseudomonas aeruginosa] Length = 399 Score = 72.5 bits (177), Expect = 3e−12 Identities = 53/149 (35%), Positives = 81/149 (53%) Query: 14 VIAAAAFILLITIGMRMTLGLFVQPVVNTTELNIAQFSLIITVFQLMWGVLQPLSGALAD 73 ++ + A IL +++G+R   GLF+ P+          F+  I +  L+WG+ QP +GALAD Sbjct: 8 ILLSGALILALSLGVRHGFGLFLAPMSADFGWGREVFAFAIALQNLVWGLAQPFTGALAD 67 Query: 74 RFGAFRVLSGGALLLVCACLIASNIPTYWGIMIAVGLLLAPGTGSGGFSIIMGQVAAQVP 133 R+GA R +  G LL     ++     +  GL ++ GLL+  G     FS+I+G V   VP Sbjct: 68 RYGAARAVLVGGLLYALGLVLMGLSQSASGLSLSAGLLIGLGLSGTSFSVILGAVGRAVP 127 Query: 134 THKRGLASGLVNAGGSAGQFLPAPLVQGL 162   +R +A G+ +A GS GQF   P   GL Sbjct: 128 AEQRSMAMGISSAAGSFGQFAMLPGTLGL 156

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS72 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 73

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 145> which encodes amino acid sequence <SEQ ID 146; NGS73>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.26    Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 3 value: −3.72 threshold: 0.0    INTEGRAL Likelihood = −3.72 Transmembrane    172-188 (171-190)    INTEGRAL Likelihood = −2.97 Transmembrane    119-135 (114-137)    INTEGRAL Likelihood = −1.86 Transmembrane    209-225 (205-225)    PERIPHERAL Likelihood = 4.88   modified ALOM score:  1.24 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.249(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty=       0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gi|11354095|pir||H81995 probable transmembrane transport protein NMA0047 [imported]-Neisseria meningitidis (group A strain Z2491) gi|7378822|emb|CAB83364.1|(AL162752) putative transmembrane transport protein [Neisseria meningitidis Z2491] Length = 405 Score = 222 bits (567), Expect = 3e−57 Identities = 116/123 (94%), Positives = 117/123 (94%), Gaps = 4/123 (3%) Query: 103 QGLVVLPEVGWTGTFYVWGAIALLILPVSWWLAGGNNGGNNAAHTQHTQATHGQSLGEAV 162 QGLVVLPEVGWTGTFYVWGAIALL LPVSWWLA    GGNNAAHTQH QATHGQSLGEAV Sbjct: 160 QGLVVLPEVGWTGTFYVWGAIALLTLPVSWWLA----GGNNAAHTQHAQATHGQSLGEAV 215 Query: 163 KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCV 222 KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGC+ Sbjct: 216 KTAFKTPSYILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCI 275 Query: 223 FSG 225 FSG Sbjct: 276 FSG 278 >gi|11351469|pir||F83484 probable MFS transporter PA1286 [imported]-Pseudomonas aeruginosa (strain PAO1) gi|9947221|gb|AAG04675.1|AE004558_4 (AE004558) probable MFS transporter [Pseudomonas aeruginosa] Length = 399 Score = 54.4 bits (130), Expect = 1e−06 Identities = 37/115 (32%), Positives = 56/115 (48%), Gaps = 10/115 (8%) Query: 111 VGWTGTFYVWGAIALLILPVSWWLAGGNNGGNNAAHTQHTQATHGQSLGEAVKTAFKTPS 170 +GW+      G +  LI+P++  +                   H QSLGEA++ A Sbjct: 160 LGWSSALLALGLLVALIVPLAGLM----------KDRPLPPQGHEQSLGEALREACAHSG 209 Query: 171 YILLHLSFFACGFHIAFLVTHLPTEVALCGLPATVASTSIAIIGLANIAGCVFSG 225 + LL L FF CGF + F+  HLP  +    LPA V +T +A++GL N+ G   +G Sbjct: 210 FWLLALGFFVCGFQVVFIGVHLPAYLVDQHLPAQVGTTVLALVGLFNVFGTYIAG 264

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS73 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 74

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 147> which encodes amino acid sequence <SEQ ID 148; NGS74>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): 0.41   Possible cleavage site: 30 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 2  value:  −1.49 threshold:  0.0   INTEGRAL Likelihood = −1.49 Transmembrane 15-31   (15-31)   INTEGRAL Likelihood = −1.28 Transmembrane 8-99   (83-99)   PERIPHERAL Likelihood = 1.59   modified ALOM score: 0.80 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----    bacterial inner membrane --- Certainty= 0.160(Affirmative)    < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||H81995 probable transmembrane transport protein NMA0047 [imported]- Neisseria meningitidis (group A strain Z2491) emb|CAB3364.1|(AL162752) putative transmembrane transport protein [Neisseria meningitidis Z2491] Length = 405 Score = 148 bits (374), Expect = 2e−35 Identities = 97/106 (91%), Positives = 103/106 (96%) Query: 1 MVLIYIFSPKTDLNFYIFAAALGFTWLATVAPTAAVTGKLFGTRYLATLFGLVMLTHQIG 60 M+LIYIFSPKTDLNFYIFAAALGFTWLATV PTA++TGKLFGTRYLATLFGL ML+HQIG Sbjct: 300 MILIYIFSPKTDLNFYIFAAALGFTWLATVTPTASITGKLFGTRYLATLFGLTMLSHQIG 359 Query: 61 GFLGSYIGGIVITQFGDYGWMWYADAVLAGTAALLVLPVREPRTAA 106 GFLGSYIGGIVITQFGDYGWMWYADA+LAGTAALL LP+REPRTAA Sbjct: 360 GFLGSYIGGIVITQFGDYGWMWYADALLAGTAALLNLPIREPRTAA 405 >pir||F83484 probable MFS transporter PA1286 [imported]-Pseudomonas aeruginosa (strain PAO1) gb|AAGO4675.1|AE004558_4 (AE004558) probable MFS transporter [Pseudomonas aeruginosa Length = 399 Score = 59.0 bits (142), Expect = 2e−08 Identities = 40/101 (39%), Positives = 61/101 (59%) Query: 1 MVLIYIFSPKTDLFYIFAAALGFTWLATVAPTAAVGKLFGTRYLATLFGLVMLTHQIG 60 +++++++ P +  + Y F  A+G  WL+TV  T      LFG R L+ L G+V L HQ+G Sbjct: 286 VIVLFLWLPLSVYSAYAFGVAMGLLWLSTVPLTNGTTLFGVRNLSMLGGIVFLFHQLG 345 Query: 61 GFLGSYIGGIVITQFGDYGWMWYADAVLAGTAALLVLPVRE 101  FLG ++GG+V  + G Y  +W    +L+  AALL  PVRE Sbjct: 346 AFLGGWLGGVVYDRTGSYDLVWQLSILLSLLAALLNWPVRE 386

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS74 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 75

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 149> which encodes amino acid sequence <SEQ ID 150; NGS75>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −5.2   Possible cleavage site: 22 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  4.45 threshold:  0.0   PERIPHERAL Likelihood = 4.45   modified ALOM score: −1.39 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.237(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: pir||S04419 type II site-specific deoxyribonuclease (EC 3.1.21.4) NgoPII- Neisseria gonorrhoeae emb|CAA368B7.1|(X52661) NgoPII restriction and modification [N. gonorrhoeae] prf||1613419A NgoPII endonuclease [Neisseria gonorrhoeae] Length = 278 Score = 240 bits (614), Expect = 4e−63 Identities = 128/129 (99%), Positives = 128/129 (99%) Query: 1 MNIIDAIINLANNPVVGVNSHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK 60 MNIIDAIINLANNPVVGV SHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK Sbjct: 1 MNIIDAIINLANNPVVGVESHSQSNNRANQAGDALEEYVKDLFSGSFNLNETQRIARHAK 60 Query: 61 VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE 120 VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE Sbjct: 61 VFSYLGNNSNPPDAMLRNGDAIEVKKIESKDSALALNSSHPKSKLSVDDSMLTKACKDAE 120 Query: 121 KWEEKDIIY 129 KWEEKDIIY Sbjct: 121 KWEEKDIIY 129

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 76

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 151> which encodes amino acid sequence <SEQ ID 152; NGS76>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −1.73   Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  9.39 threshold:  0.0   PERIPHERAL Likelihood = 9.39   modified ALOM score: −2.38 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.272(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: pir||S04419 type II site-specific deoxyribonuclease (EC 3.1.21.4) NgoPII- Neisseria gonorrhoeae emb|CAA36887.1|(X52661) NgoPII restriction and modification [N. gonorrhoeae] prf||1613419A NgoPII endonuclease [Neisseria gonorrhoeae] Length = 278 Score = 268 bits (687), Expect = 2e−71 Identities = 136/136 (100%), Positives = 136/136 (100%) Query: 1 LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM 60 LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM Sbjct: 143 LAMVYGIDYCADAECYLKIKNQIKEGIGNIGGIQFAETKELGRVNRIDPLNITYLRVRGM 202 Query: 61 WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP 120 WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP Sbjct: 203 WGIENPWFVFNYIYQRNMEKSFNFMAIINEDKWNSFNNTDKLLAIQDSKLAISDIKIKNP 262 Query: 121 NNPARLRNAKLITYHL 136 NNPARLRNAKLITYHL Sbjct: 263 NNPARLRNAKLITYHL 278

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 77

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 153> which encodes amino acid sequence <SEQ ID 154; NGS77>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.51   Possible cleavage site: 58 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  3.18 threshold:  0.0   PERIPHERAL Likelihood = 3.18   modified ALOM score: −1.14 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.127(Affirmative) <succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir|||CTNHP2 site-specific DNA-methyltransferase (cytosine-specific) (EC 2.1.1.73) NgoPII-Neisseria gonorrhoeae emb|CAA30038.1|(X06965) NgoPII methylase (AA 1-341) [Neisseria gonorrhoeae] emb|CAA3688B.1|(K52661) NgoPII restriction and modification [Neisseria gonorrhoeae] gb|AAA170419.1|(L14564) cytosine methylase [Neisseria gonorrhoeae] prf||1613419B NgoPII methylase [Neisseria gonorrhoeae] Length = 341 Score = 682 bits (1761), Expect = 0.0 Identities = 341/341 (100%), Positives = 341/341 (100%) Query: 1 MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE 60 MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE Sbjct: 1 MQNSSPTTYNPMKIISLFSGCGGLDLGFEKAGFEIPAANEYDKTIWATFKANHPKTHLIE 60 Query: 61 GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL 120 GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL Sbjct: 61 GDIRKIKEEDFPEEIDGIIGGPPCQSWSEAGALRGIDDARGQLFFDYIRILKSKQPKFFL 120 Query: 121 AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI 180 AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI Sbjct: 121 AENVSGMLANRHNGAVQNLLKMFDGCGYDVTLTMANAKDYGVAQERKRVFYIGFRKDLEI 180 Query: 181 KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR 240 KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR Sbjct: 181 KFSFPKGSTVEDKDKITLKDVIWDLQDTAVPSAPQNKTNPDAVNNNEYFTGSFSPIFMSR 240 Query: 241 NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG 300 NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG Sbjct: 241 NRVKAWDEQGFTVQASGRQCQLHPQAPKMEKHGANDYRFAAGKETLYRRMTVREVARIQG 300 Query: 301 FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER 341 FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER Sbjct: 301 FPDNFKFIYQNVNDAYKMIGNAVPVNLAYEIAAAIKKTLER 341

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 78

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 155> which encodes amino acid sequence <SEQ ID 156; NGS78>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −8.33   Possible cleavage site: 24 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  2.17 threshold:  0.0   PERIPHERAL Likelihood = 2.17   modified ALOM score: −0.93 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.220(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||H82000 hypothetical protein NMA0089 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB83405.1|(AL162752) hypothetical protein NMA0089 [Neisseria meningitidis Z2491] Length = 226 Score = 422 bits (1085), Expect = e−117 Identities = 217/228 (95%), Positives = 220/228 (96%), Gaps = 2/228 (0%) Query: 1 MERYKNAVRKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICFRQEFKDRNRLYDSI 60 MERYKNAV KDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDIC +Q FKD N LY+SI Sbjct: 1 MERYKNAVGKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICLQQAFKDGNWLYNSI 60 Query: 61 QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA 120 QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA Sbjct: 61 QPQTNPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFA 120 Query: 121 GGKDAQFDAAGKVLMKVFPKKPKSTPSVQYNQKWIFRELSNINNFRNRLAHHEPICFSFK 180 GGKDAQFDA GKVLMKVFPKKPKSTPSVQ+NQKWIFRELSNINNFRNRLAHHEPIC  FK Sbjct: 121 GGKDAQFDATGKVLMKVFPKKPKSTPSVQHNQKWIFRELSNINNFRNRLAHHEPIC--FK 178 Query: 181 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL 228 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL Sbjct: 179 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSHFSDQVIAVCDEIDKL 226 >ref|NP_053274.1|Hypothetical gene [Agrobacterium tumefaciens] dbj|BAA87659.1|(AB016260) Hypothetical gene [Agrobacterium tumefaciens] Length = 380 Score = 43.6 bits (102), Expect = 0.002 Identities = 53/215 (24%), Positives = 86/215 (39%), Gaps = 42/215 (19%) Query: 5 KNAVRKDKAAELYLLNLSLSRELFHVVSIFEIVLRNKIDICFRQEFKDRNRLYDSIQPQT 64 K    ++ A  LYL N  +++   + +++ E+ LRN +D      F Sbjct: 55 KGGNHEEYAMALYLYNARVAKAFLYPLNVAEVTLRNAVDGILVARFG------------- 101 Query: 65 NPALKYQGCFLRNGTKESAELIKVALSKIQNNSGGKFDHNQLVAGLGFGFWRYLFAGGKD 124   A  +Q    R+ T     L    L K    +G     +Q+VA L F FW  LF Sbjct: 102 --ANWHQDATFRDQTLTGNGL--ATLDKAIQRAGAGAARDQIVATLTFDFWSNLFR---- 153 Query: 125 AQFDAAGKVLMKVPKKPKSTPSVQYNQKWIFRELSN----INNFRNRLAHHEPICFSFK 180  ++    +  + +      + P +Q+ +    +E+ N    IN FRNR+AHHEP+ Sbjct: 154 PEYGGLWRTTVNI------AFPHLQHGESR--QEIQNINKPINFRNRVAHHEPVL---- 201 Query: 181 GAIKDTGYARNIHQSIFELLNYMDVDTASVFSSFS 215     D     +IH  I  L+     +TA+   H S Sbjct: 202 ----DLNVT-DIHAKIVRLIELRCAETATWMKHHS 231

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS78 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 79

A DNA sequence was identified in N.gonorrhoeae <SEQ D 157> which encodes amino acid sequence <SEQ ID 158; NGS79>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): 2.07   Possible cleavage site: 17 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 18 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  9.49 threshold:  0.0   PERIPHERAL Likelihood = 9.49   modified ALOM score: −2.40 Score for OM-PP discrimination: −11.72 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −11.72 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 1.17242 Periplasmic space? Score: 1.17242 ----- Final Results -----   bacterial periplasmic space --- Certainty= 0.932(Affirmative) < succ>    bacterial outer membrane --- Certainty= 0.240(Affirmative)    < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

A homolog (amino acids 23-85) was found in serogroup A N.meningitidis but not in serogroup B, so NGS79 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 80

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 159> which encodes amino acid sequence <SEQ ID 160; NGS80>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −8.49   Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  4.98 threshold:  0.0   PERIPHERAL Likelihood = 4.98   modified ALOM score: −1.50 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.428(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||E81080 conserved hypothetical protein NMB1466 [imported]-Neisseria meningitidis (group B strain MD58) gb|AAF41823.1|(AE002496) conserved hypothetical protein [Neisseria meningitidis MC58] Length = 243 Score = 148 bits (375), Expect = 7e−35 Identities = 82/189 (43%), Positives = 109/189 (57%) Query: 120 VDRMFNMAGNHFARLGISSGSGVHYWNARDFSEQAFHAEVGYRYRNSRLEWGFRPFVKQNR 179 + R  N   +HF   GISG GVHYW+ +DFSEQ+     GY+ R+    +G  PFV+QN Sbjct: 1 MSREINAGRHHFLYGGISGGGVHYWDNKDFSEQSLRLSFGYKNRSVTRSFGIVPFVEQNL 60 Query: 180 LGNNRYTANTGIVLDYSRRLNEKWRSTQSFQYGRKQYHDEYIAKRYNSKTISVSGTFSYY 239 LG +RY    G   D+S+RL+E+WR T +     K Y ++  A RY+S       T  Y Sbjct: 61 LGGSRYNFVGGFNADFSQRLSERWRLTLNAGNMWKHYQEDRTAARYDSHMPLAGATLMYS 120 Query: 240 AMSAWQLYGGISGNFDNTVEKEQASBRYGVSLGTVKILDGGLGLKLGAGYTKRIFKAPAT 299 A   W LYGG     + T E EQAS R G+ +G VK  DGGLGL+    YT+R+F AP T Sbjct: 121 APKDWLLYGGADWSHNITKEAEQASIRKGLRVGAVKTFDGGLGLRANLRYTRRMFDAPGT 180 Query: 300 LIYNFTRRD 308 ++Y F R+D Sbjct: 181 IVYRFPRKD 189 >gb|AAD11779.1|(AF118122) putative outer membrane protein OmpU [Neisseria meningitidis] Length = 488 Score = 72.1 bits (176), Expect = 7e−12 Identities = 71/300 (23%), Positives = 128/300 (42%), Gaps = 17/300 (5%) Query: 3 EAADLYRELLSERPDLVYPRFDLGVMLFEDKQYREALVQLHRAE-EVLPPDMRQLAREYI 61 EA   YREL++ +PD    R  L   LF+++Q   A  Q  R + E LPP + +    Y Sbjct: 136 EAISHYRELIAAQPDAPAVRMRLAAALFDNRQNEAAADQFDRLKAENLPPQLMEQVELYR 195 Query: 62 RQAEAVQAWHPSFNMNYEQTDNVNNASLSRDIVINGRKWIKSEDSLPKRANT--IRYELG 119 +      AW  +   +  +  N+N A   +       KW     + PK+ +G  + Y LG Sbjct: 196 KALRERDAWKVNGGFSVTREHNINQAPKRQQR----GLW-----TFPKQVDGTAVNYRLG 246 Query: 120 VDRMFNMAGNHFARLGISGSGVHYWNARDFSEQAFHAEVGYRYRNSRLEWGFRPFVKQNR 179 ++ +++    +   G   SG  Y   + F++       G  + + R + G   F ++ Sbjct: 247 AEKKWSLKNGWYTTAGGDVSGRVYPGNKKFNDMTAGVSGGIGFADRRKDAGLAVFHERRT 306 Query: 180 LGNNRYTANTGIVLDYSRRLNEKWRSTQSFQYGRKQYHDEYLAKRYNSKTISVSGTFSYY 239  GN+ Y+   G  L ++R    KW++  S ++GR +        R ++  + +S +  +Y Sbjct: 307 YGNDAYSYTNGARLYFNRWQTPKWQTLSSAEWGRLK---NTRRARSDNTHLQISNSLVFY 363 Query: 240 AMSAWQLYGGISGMFD-NTVEKEQASRRYGVSLGTVKILDG-GLGLKLGAGYTKRIFKAP 297   +     GG+    + N  ++     RYG+     +   G GL   L  G  KR ++ P Sbjct: 364 RNARQYWMGGLDFYRERNPADRGDNFNRYGLRFAWGQEWGGSGLSSLLRLGAAKRHYEKP 423

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 81

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 161> which encodes amino acid sequence <SEQ ID 162; NGS81>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −6.25   Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  7.05 threshold:  0.0   PERIPHERAL Likelihood = 7.05   modified ALOM score: −1.91 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.232(Affirmative)      < succ>

The protein has homology with the following sequences in the databases: gi|10803654|ref|NP_046052.1|putative ISH4 transposase [Halobacterium sp. NRC-1] gi|7484109|pir||T08324 probable transposase H1306-Halobacterium sp. (strain NRC-1) insertion sequence ISH4 plasmid pNRC100 gi|2822385|gb|AAC82891.1|(AF016485) putative ISH4 transposase [Halobacterium sp. NRC-1] gi|10580476|gb|AAG19350.1|(AE005029) Vng0918h [Halobacterium sp. NRC-1] Length = 294 Score = 52.1 bits (124), Expect = 4e−06 Identities = 36/139 (25%), Positives = 63/139 (44%), Gaps = 7/139 (5%) Query: 31 CPHCQSTHFVKNGKDCGNQRFLCRDCKKSFVEQTGTILYNTQKDIEVWEKYIHCMIE-KY 89 CP C++   ++ G     QR+LC+DC ++F +QTGT+ ++   +  W   ++  I Sbjct: 28 CPSCRAESVIRYGSYRVFQRYLCKDCDRTFNDQTGTVFEHSAVALRKWFLAVYTYIRLNT 87 Query: 90 PLRKCAEICKINLATAFTWRHKILDALQNMMNEVELDGIVQADETYSTISYKGHHKNFNL 149  +R+      ++  T +    + L AL        L+G V+ DE Y     KG  ++ Sbjct: 88 SIRQLDAEIDVSYKTVYRRVQRFLRALD--APRPHLEGPVEIDEFYVKAGLKGRERD--- 142 Query: 150 PRPAHKRGTRATKRGISKE 168  +P+  RG     RG   E Sbjct: 143 -QPSRSRGLSTRGRGTYAE 160

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 82

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 163> which encodes amino acid sequence <SEQ ID 164; NGS82>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.66   Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1  value:  −0.85 threshold:  0.0   INTEGRAL Likelihood = −0.85 Transmembrane 76-92 (76-92)   PERIPHERAL Likelihood = 1.75   modified ALOM score: 0.67 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----   bacterial inner membrane --- Certainty= 0.134(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|586070|sp|Q07605|T4BA_BACCO RESTRICTION ENZYME BGCI ALPHA SUBUNIT [INCLUDES: ADENINE-SPECIFIC METHYLTRANSFERASE ACTIVITY] gi|1075788|pir||A53125 restriction enzyme BcgI alpha chain-Bacillus coagulans gi|304140|gb|AAA16626.1|(L17341) restriction endonuclease alpha subunit [Bacillus coagulans] Length = 637 Score = 91.4 bits (226), Expect = 1e−17 Identities = 78/256 (30%), Positives = 123/256 (47%), Gaps = 42/256 (16%) Query: 1 MFALAASNMILRGDGKANLHQSSCFMTDFQDLIKNPKPETGLKRPNVGFLNPPYAQSKSD 60 +F  +A +NMILRGDGK+NL + +C    F + I N     G+   N   +NPPY+Q+K+D Sbjct: 394 LFTIATTNMILRGDGKSNLIRDNCLT--FDNTIMN---GYGI---NKILMNPPYSQAKND 445 Query: 61 AELH--ELYFVKEMLKMLAEGGTGIAIIPVSCVIAPSK----AKSEIVKYHRLKAVMSMP 114    H  EL F+++ L+ML  GG   AI+P S ++  ++     K +I+K H L+ V+++ Sbjct: 446 QTQHLSELSFIQQALEMLVVGGKLCAIVPQSTMVGKNRHDKARKKQILKQHTLETVITLN 505 Query: 115 SELFYPVGTVTCIVVFEAHKPHFQTVVIDPDTQEEISTKKACENTWFGYWRDDGFEKTKH 174  + F+ VG   CIV+F+A   H +                  ++  F  + DDG    KH Sbjct: 506 KDTFHGVGVNPCIVIFKAGIKHPEN-----------------KRVSFVNFEDDGHVVRKH 548 Query: 175 LGRIDLYDRWQGIKARWLEHYL-----NNEVHTGESVTAFVTDNDEWVAEAYLETDYSKI 229 +G +       G +    EH L     + +  T   V   + D DEW+   Y   D Sbjct: 549 VGLVG-----DGTEKGKREHLLAVLAGDEDDGTDLIVKTAIKDTDEWLHSFYYFND-GIP 602 Query: 230 TRADFEQVVREFALFQ 245 +  DF + V  +  FQ Sbjct: 603 SEDDFYKTVANYLTFQ 618

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 83

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 165> which encodes amino acid sequence <SEQ ID 166; NGS83>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −8.04   Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1  value: −1.44 threshold:  0.0   INTEGRAL Likelihood = −1.44 Transmembrane 55-71 (55-71)   PERIPHERAL Likelihood = 4.03   modified ALOM score: 0.79 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----      bacterial inner membrane --- Certainty= 0.157      (Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|586071|sp|Q07606|T4BB_BACCO RESTRICTION ENZYNE BGCI BETA SUBUNIT gi|1075789|pir||B53125 restriction enzyme BcgI beta chain-Bacillus coagulans gi|304141|gb|AAA16627.1|(L17341) restriction endonuclease beta subunit [Bacillus coagulans] Length = 341 Score = 44.0 bits (103), Expect = 0.002 Identities = 46/195 (23%), Positives = 79/195 (39%), Gaps = 23/195 (11%) Query: 4 LQEIFDVSYGSKLDLNKMSSFNPTINFVGRSGKNNGVTASVDLLKNTKPYPAGLLTVALG 63 + ++FDV  G  +D NK         ++R    NG    +D  K  K Y   L  + +G Sbjct: 12 ISDLFDVVIGKTIDGNKAQRNENGTPYITRKATRNGFEFMIDGEKE-KLYSGKLPVITIG 70 Query: 64 GSVLSTFLQNKPFYTAQNVAVLNPKTEMTEQQKLFYCAAIFANAYRFSACGREANRT-LR 122       F+Q   F+T   V +  PK ++     L Y   +  NA +  +     N T L+ Sbjct: 71 NETSKPFVQEFHFFTGTKVNICIPKLDLNRNH-LLYITTMIENATKMFSYSYTINSTRLK 129 Query: 123 QL--FVPSLDEIPSW--------------VESVNLNPSAGVTEPKLKESLDLPVVRQSKR 166  L   +P   E P W               ++ ++  + GV++ +  + L         + Sbjct: 130 SLKILLPIKGEEPDWDYMNTYISKILSNMEKNFDVQQNDGVSDLRSLKDLSW----SQFK 185 Query: 167 LPEIFTIQNGIAATK 181 +DEIF+I +G+  TK Sbjct: 186 MDEIFSINSGVRLTK 200

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 84

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 167> which encodes amino acid sequence <SEQ ID 168; NGS84>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): 3.15   Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  1.22 threshold:  0.0   PERIPHERAL Likelihood = 1.22   modified ALOM score: −0.74 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.072(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|2495432|sp|P55409|Y4DJ_RHISN HYPOTHETICAL TRANSCRIPTIONAL REGULATOR Y4DJ gi|7465604|pir||T02773 y4dJ protein-Rhizobium sp. plasmid pNGR234a gi|2182353|gb|AAB91639.1|(AE000069) Y4dJ [Rhizobium sp. NGR234] Length = 77 Score = 44.4 bits (104), Expect = 7e−04 Identities = 25/61 (40%), Positives = 36/61 (58%) Query: 92 KAGGETFVSLRKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLE 151 K  G  F  LR +KG TQ E+   +G  Q YLS +E  +++    T+ +LA ALGVS +E Sbjct: 5 KLVGSNFARLREEKGLTQEEEARSGFSQQYLSSLERGRRNPTVITLYELAQALGVSHVE 64 Query: 152 V 152 + Sbjct: 65 L 65

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 85

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 169> which encodes amino acid sequence <SEQ ID 170; NGS85>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −6.09   Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  2.92 threshold:  0.0   PERIPHERAL Likelihood = 2.92   modified ALOM score: −1.08 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.480(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 86

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 171> which encodes amino acid sequence <SEQ ID 172; NGS86>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −2.92   Possible cleavage site: 21 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1  value:  −2.76 threshold:  0.0   INTEGRAL Likelihood = −2.76 Transmembrane 179-195   (179-195)   PERIPHERAL Likelihood = 2.17   modified ALOM score: 1.05 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----      bacterial inner membrane --- Certainty= 0.210      (Affirmative) < succ>

The protein has homology with the following sequences in the databases: >sp|Q05205|PPB_LYSEN ALKALINE PHOSPHATASE PRECURSOR (APASE) pir||A42467 alkaline phosphatase (EC 3.1.3.1) phoA precursor-Lysobacter enzymogenes emb|CAA39978.1|(X56656) alkaline phosphatase [Lysobacter enzymogenes] Length = 539 Score = 37.5 bits (86), Expect = 0.40 Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 8/82 (9%) Query: 189 VALGLQAYWDVAGANNGATGQSPNIKTAQVPAKITRRNADGTTDTFGGGSARKSAAASVS 248 V  GL A W+V+ A          +  AQV  +++ R+  GT D +  G+A   A AS S Sbjct: 458 VLRGLMA-WNVSSA------AGKTLTGAQVKLQVSDRST-GTYDLYRAGAAWTEANASYS 509 Query: 249 GIEAGKKVTAVIPAVRGAVAYA 270 G+  G K+ +V+P+  GA + A Sbjct: 510 GVSLGSKIGSVVPSATGAQSIA 531

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 87

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 173> which encodes amino acid sequence <SEQ ID 174; NGS97>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): 0.18   Possible cleavage site: 35 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  1.70 threshold:  0.0   PERIPHERAL Likelihood = 1.70   modified ALOM score: −0.84 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.138(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|12514207|gb|AAG55499.1|AE005289_17 (AE005289) unknown protein encoded by cryptic prophage CP-933M [Escherichia coli O157:H7] gi|12514720|gb|AAG55907.1|AE005324_10 (AE005324) unknown protein encoded by prophage CP-933N [Escherichia coli O157:H7] Length = 108 Score = 30.9 bits (69), Expect = 9.1 Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 3/55 (5%) Query: 1 MAAPVSLEEFKQRIGVEHDRRDDFFLSVIDGVSAAAEAYIGRSLLAADYVGRYDG 55 M A ++LEE K  + V+HD  DD  +  +   +A   AYI  S    D V R DG Sbjct: 1 MTALLTLEEIKAHLRVDHDADDDMLMDKVRQATAVLLAYIQGS---RDKVIREDG 52

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 88

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 175> which encodes amino acid sequence <SEQ ID 176; NGS88>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.69   Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  6.05 threshold:  0.0   PERIPHERAL Likelihood = 6.05   modified ALOM score: −1.71 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.227(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 89

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 177> which encodes amino acid sequence <SEQ ID 178; NGS89>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −4.77   Possible cleavage site: 26 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  1.38 threshold:  0.0   PERIPHERAL Likelihood = 1.38   modified ALOM score: −0.78 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.284(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|9634142|ref|NP_037684.1|gp24 [Enterobacteria phage HK022] gi|6863134|gb|AAF30375.1|AF069308_23 (AF069308) gp24 [Enterobacteria phage HK022] Length = 1183 Score = 44.9 bits (102), Expect = 0.006 Identities = 38/127 (29%), Positives = 64/127 (49%), Gaps = 11/127 (8%) Query: 851 NKALRDKINLIDGNGAGSVNERVEAVRSTADGNAAAVQTHARSI---NG-LEAQYTVK-- 904 NKA  + +N    +   +   ++  + +T +GN +A+ T+A++I   NG L A Y +K Sbjct: 989 NKASINSLNQTFSDYQQATATQINGITATVNGNTSAITTNAQAIANVNGDLSAMYNIKVG 1048 Query: 905 VDANGK--VAGFGLATTPKNGTPESKFIVNADRFGI-GAAGKADVFPFVVDTQKNRVGIN 961 V +NG+   AG G+         +S+ I  ADRF +  AAG +   PFV+  Q  +  I Sbjct: 1049 VSSNGQYYAAGMGIGVENTPSGMQSQVIFLADRFAVTTAAGNSVALPFVI--QNGQTFIR 1106 Query: 962 GELVVNG 968    + +G Sbjct: 1107 ASFIQDG 1113

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 90

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 179> which encodes amino acid sequence <SEQ ID 180; NGS90>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −2.82   Possible cleavage site: 24 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 4  value:  −9.66 threshold:  0.0   INTEGRAL Likelihood = −9.66 Transmembrane 321-337   (317-349)   INTEGRAL Likelihood = −6.48 Transmembrane 351-367   (340-371)   INTEGRAL Likelihood = −5.73 Transmembrane 907-923   (903-926)   INTEGRAL Likelihood = −0.00 Transmembrane 430-446   (430-446)   PERIPHERAL Likelihood = 2.17   modified ALOM score: 2.43 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----      bacterial inner membrane --- Certainty= 0.486      (Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|12514839|gb|AAG56002.1|AE005332_9 (AE005332) putative tail component of prophage CP-933X [Escherichia coli O157:H7] Length = 1026 Score = 111 bits (279), Expect = 3e−23 Identities = 78/274 (28%), Positives = 146/274 (52%), Gaps = 10/274 (3%) Query: 69 AAGNQAQQASEKVRAEVGKIGSGLSGLTKLLAGLATADFAKSVLDTADAMQSINSQVRQV 128 AA  + ++A  ++ +++ +I +   G+T   AG   A     ++  AD   S+N++++Q Sbjct: 45 AAAREQRRALAELHSQLTEIRASAVGMTGAFAG---AFATGHLISLADEWSSVNARLKQA 101 Query: 129 TSSETEYLAVQQQLLDTANRTRASLESTANLYVSTSRALKDYGYTQQEILKFTEAANNAM 188 + S  E+ + Q+ L+D + RT  +    A L+  ++ ++++YGY+  ++LK TEA +  + Sbjct: 102 SQSSDEFASSQKVLMDISQRTGTAFSDNAALFARSAASMREYGYSADDVLKVTEAISTGL 161 Query: 189 TIGGVGAQQQAAALMQLSQALGSGVLQGDEFKSISEAAPILLDTIAEYMGKSRDEIKKLG 248  I G    +  + + Q SQAL  GVL+G+EF S++E+   ++  +A  MG +R ++K + Sbjct: 162 KISGASTAEAGSVITQFSQALAQGVLRGEEFNSVNESGDRIVRALAAGMGVARKDLKAMA 221 Query: 249 SEGKLTADVIFKAISGASEKFGEQAAKMPVTMGQALTVFSNNWQSMVSKLLNDSGTMSGI 308  +GKLTAD +  A+        ++ A MP T+  ++T   N + + V       G  + Sbjct: 222 DDGKLTADKVVPALISQLGILRDEYAAMPETVSSSITKVENAFMAWV-------GGANEA 274 Query: 309 AAVIKLIADNLNLVVPIVAGFAVAVAAAVAPTLA 342 + V K ++  LN V   +   A AV A VA  +A Sbjct: 275 SGVTKTLSGMLNGVAGQIDNVATAVGALVAVGVA 308

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 91

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 181> which encodes amino acid sequence <SEQ ID 182; NGS91>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −0.63   Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  0.16 threshold:  0.0   PERIPHERAL Likelihood = 0.16   modified ALOM score: −0.53 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.250(Affirmative) < succ>

The protein has homology with the following sequences in the databases: (AF237934) putative integrase/recombinase [Pasteurella multocida] Length = 329 Score = 449 (206.9 bits), Expect = 4.4e−91, Sum P(2) = 4.4e−91 Identities = 93/196 (47%), Positives = 129/196 (65%) Query: 56 IFADLIRRYLSEVTPSKRGAREESYRIGRALKTPLAKVRLADLRPQDFADWRDQRLQEVS 115 IF D+I RY +EV+ +K+GAR E R+ R L+  ++  + + DLR +DF +W   RL EVS Sbjct: 55 IFRDVIERYQNEVSITKKGARNEIIRLNRFLRYDISNLYIRDLRKEDFEEWIRIRLTEVS 114 Query: 116 PTSVGRELTTLSAVCEHAMKEWGLLRENPVRKISKPKKSRARTRRPTEQEIADICAALLY 175   SV REL T+S+V   A+ +WG +  +P+  I KPK S  R  R +EQ+I  I     Y Sbjct: 115 DASVRRELVTISSVLTTAINKWGYISRHPMTGIEKPKNSAERKERYSEQDIKTILETARY 174 Query: 176 RPNEKPKMAVQRVAVAVLFAIETAMRAGEICGLKWADVNMRRRIAHLPITKNGDSRDVPL 235   ++ P    QRVA+A+LFAIETAMRAGEI  +KW +V + +RI HLP TKNG SRDVPL Sbjct: 175 CEDKLPITLKQRVAIAMLFAIETAMRAGEIASIKWDNVFLEKRIVHLPTTKNGHSRDVPL 234 Query: 236 SLRAAELIEQLRGIDD 251 S RA  LI +++ +++ Sbjct: 235 SQRAVALILKMKEVEN 250 Score = 248 (114.3 bits), Expect = 4.4e−91, Sum P(2) = 4.4e−91 Identities = 48/76 (63%), Positives = 57/76 (75%) Query: 254 VFSLDAKSLDVLFRRARDNCGIQGLHFHDTRREALTRLSKKVPVEVLAKISGHRDLRILL 313 VF    +SL   FR  +  CG++ LHFHDTRREALTRLSKKV V  LAKISGHRDLRIL Sbjct: 254 VFQTTPESLSTTFRVLKKECGLEHLHFHDTRREALTRLSKKVDVMTLAKISGHRDLRILQ 313 Query: 314 NVYYRPDMADIAKMLD 329 N YY P+M+++A +LD Sbjct: 314 NTYYAPNMSEVANLLD 329

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 92

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 183> which encodes amino acid sequence <SEQ ID 184; NGS92>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −7.85   Possible cleavage site: 25 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1  value:  −8.33 threshold:  0.0   INTEGRAL Likelihood = −8.33 Transmembrane 6-22 (1-25)   PERIPHERAL Likelihood = 5.99   modified ALOM score: 2.17 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----      bacterial inner membrane --- Certainty= 0.433      (Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|963205|ref|NP_048840.1|A484L [Paramecium bursaria Chlorella virus 1] gi|7461623|pir|T17986 hypothetical protein A484L-Chlorella virus PBCV-1 gi|1620155|gb|AAC96851.1|(U42580) A484L [Paramecium bursaria Chlorella virus 1] Length = 155 Score = 31.6 bits (70), Expect = 3.5 Identities = 20/72 (27%), Positives = 36/72 (49%) Frame = +1 Query: 52 LQINLKMLEKRIDFLVENIDKYYQQYGSYPNNFDFISTKTDFTTESYCDFWDKNIAGYGN 231 + +NLKM    I F    +DKY +QY +Y  N  F  T+ +   +   ++ + +I    N Sbjct: 23 IAVNLKMNGVSIPF----VDKYSKQYPTYTKNALFHVTRFNNAYQKTFEYKNISIDTINN 78 Query: 232 CYFVKNDKDYTI 267  + +++D  Y I Sbjct: 79 LFSIRDDVLYNI 90

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 93

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 185> which encodes amino acid sequence <SEQ ID 186; NGS93>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −5.08   Possible cleavage site: 14 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  0.79 threshold:  0.0   PERIPHERAL Likelihood = 0.79   modified ALOM score: −0.66 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.320(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gb|AAG22017.1|AF288038_2 (AF288038) putative HsdR ]Streptococcus thermophilus] Length = 740 Score = 674 bits (1738), Expect = 0.0 Identities = 364/746 (48%), Positives = 489/746 (64%), Gaps = 40/746 (5%) Query: 14 NENSRVKIPAVLHLMRLGYDYLSLKNANW---DRQTNIFPEIFVDSLCRINPDLPPDDAR 70 +E +RV+IPA  HLMRLGY YL          D +TNI   IF +   + N      D Sbjct: 8 SELTRVQIPAAFHLMRLGYTYLPHNGKEIMGRDPETNILISIFREQFLKFNNYATDLDVE 67 Query: 71 RLLADIRLELDNEDLGQKFYERLTNQSGGKKLIDFQNFDNNSFHVVTELPCINGDEAFRP 130 R L +I++ELD DLG+ FY R+ + SG    +D++N +NN+FH+  E+ C NG + FRP Sbjct: 68 RELNNIKIELDQNDLGRAFYNRIVSDSG-PTYVDWENPENNTFHLALEVTCQNGGDEFRP 126 Query: 131 DIALLVNGMPLVFIEVKKPN----NKGGIGEERERMGKRAKNPKFRRFINITQFMIFSNN 186 DI + +NG+PL +IEVK+PN     K  I  E+ R   R +N +FRRF NITQ + FS+N Sbjct: 127 DIVIFINGLPLSYIEVKQPNAIRDGKTAIQSEQSRTAVRFENRRFRRFNNITQLISFSDN 186 Query: 187 MEYDDGATEPAQGAFYASSACGKPVFNYFREEHKXXXXXXXXXXXXXXXXXVLQDNNLPV 246 + Y  G  +  QG+FY S+A  K  FN F+EE +                 VL+D N Sbjct: 187 LPYISGQGQQKQGSFYCSNAFSKTKFNAFKEEREEELIYSIRSLGEEEIDAVLKDVNRFA 246 Query: 247 IKHSPEFISNKSPDTPTNRILTSLLCRERLSFLLQHGLTYVK--ASQGLVQ--KHIMRYP 302 +K  PEF +N+ P TP N  ++SL  ++RL FLL++GL YV+  +  G +Q  KH+MRYP Sbjct: 247 LKSQPEFKTNQDPSTPCNTFISSLYQKKRLLFLLRYGLAYVEEHSKDGTIQLQKHVMRYP 306 Query: 303 QLFATLAIEKHLANGGKKGVIWHTQGSGKTALAYYNTRYLTHYYAKQGIVPKFYFIVDRL 362 Q FAT AIE  +  G +KGVIWHTQGSGKTAL+Y+N RYLT+Y++KQGIVP+FYF+VDRL Sbjct: 307 QFFATKAIEDAIGKGVRKGVIWHTQGSGKTALSYFNIRYLTNYFSKQGIVPQFYFVVDRL 366 Query: 363 DLLKQAQREFTARDLVVHTIDSREAFAADIKSAQTLHNHAGKAEITVVNIQKFQDDPDVV 422 DL QA REFT R L V  I+S           Q L+      ++ VVNIQKF+D+ D+ Sbjct: 367 DLADQATREFTKRGLKVKRINS----------PQELNEKHDAYQVAVVNIQKFKDNSDLT 416 Query: 423 ARNDYDLAIQRVYFLDEVHRSYNPKGSFLANLNQSDVNAVKIGLTGTPLI-----GVTA- 476   + YDL  Q +YF+DE HRSYN KGS+L NL  +D NA+KI LTGTPLI     G T Sbjct: 417 DHSGYDLNRQNIYFIDEAHRSYNEKGSYLPNLYNADKNAIKIALTGTPLITYKKDGKTKE 476 Query: 477 GNVNTRELFGDYIHKYYYNASIADGYTLRLIREEIGSRYKAQLQEALAQLEIEKGSFDRK 536  +  TR++FGDYIHKYYYN SI DG+TLRL+RE+I + YK  LQ      EI +G   + Sbjct: 477 SHATTRDIFGDYIHKYYYNQSIDDGFTLRLMREDIETSYKETLQTI--NEEILRGDLSKD 534 Query: 537 EIYAHPHFVHPMLDYILDDFAKFRKTN-QDESLGAMVVCDSAEQARQL---FEHFQTASD 592 +I+AHP +V PMLG+IL+DF + R     D+S+G M+VCDS++QAR++    E  ++  + Sbjct: 535 DIFAHPRYVSPMLDFILEDFNRARDVVFDDDSIGGMIVCDSSKQAREIEKQLEERRSRGE 594 Query: 593 HNFTAALILHDVGTKEERDQWVKDFKAGKIDILFVYNMLLTGFDAPRLKKLYLGRLIKAH 652  N T+ALILHD G KE +   V+ ++ GKID++ VY+MLLTGFDAPRLK+LYLGR IKAH Sbjct: 595 TNITSALILHDEGDKEYKKDRVESYREGKIDLVIVYSMLLTGFDAPRLKRLYLGRKIKAH 654 Query: 653 NLLQTLTRVNRTYKSYRYGYVVDFADIEREFDKTNRAYWDELSEN-----LGDEIGS-YS 706 NLLQTLTRVNR YK Y++GYV+DFADI +EFDKTNRAY +EL+ E      G+++ + + Sbjct: 655 NLLQTLTRVNRPYKDYQFGYVIDFADISKEFDKTNRAYLEELNQEYDPKNTGEDVENVFG 714 Query: 707 QLFKTAEEIEQEIADIKNALFDFDTE 732  LF +A+EI +++   +  L ++ TE Sbjct: 715 SLFVSADEISKQLEKSETILMNPTE 740

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 94

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 187> which encodes amino acid sequence <SEQ ID 188; NGS94>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.19   Possible cleavage site: 35 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  5.73 threshold:  0.0   PERIPHERAL Likelihood = 5.73   modified ALOM score: −1.65 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.302(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|10717100|gb|AAG22014.1|AF288037_3 (AF288037) putative HsdS [Streptococcus thermophilus] Length = 402 Score = 154 bits (389), Expect = 2e−36 Identities = 123/348 (35%), Positives = 168/348 (47%), Gaps = 48/348 (13%) Query: 73 GKTAFVDILDDGEVAFGSTEFIVLRAKNET--NPEFLYYFAISPDFRKRAIECMEGTSGR 130 GKT    ++ DGE ++     IV    +E+    +FLYYF  +  F         G++ + Sbjct: 74 GKT----VIFDGEDSYFQDSNIVWIENDESKVTNQFLYYFLQTNPFIT-----TNGSTIK 124 Query: 131 QRVNENALKTLELPIPEPQIQQSIAAVLSALDKKIALNKQINARLEEMAKTLYDYWFVQF 190 +  N+N   T    +P  Q Q  I   +L  LDKKI +N QIN  LE MAKTLYDYWFVQF Sbjct: 125 RLYNDNLRDTKIPNVPSIQQQNQITDILGTLDKKIQINNQINQELEAMAKTLYDYWFVQF 184 Query: 191 DFPDANGKPYKSSGGDMVFDETLKREIPKGWGSIELQSCL---AKIPNTTKILNKDIKDF 247 DFPD NGKPYKSSGG MV++  LKREIP+GWG+ +L S L    +  N  K  N++ K + Sbjct: 185 DFPDQNGKPYKSSGGKMVYNPELKREIPEGWGAEKLSSLLKIGKETTNPKKFPNEEFKYY 244 Query: 248 --------GKYPVVD----QSQDFICGFTNKEKSILNPQDAHIIFGDHTRIVKLVNFQYA 295         G Y +      +S  F     +   S LNP    +I+      +    F Sbjct: 245 SIPEFDTTGTYSLERGESIKSNKFKFKVEKNDLLVSKLNPWFNRVIYNLEENAIASTEF--- 301 Query: 296 RGADGTQVILSNNERMPNYLFYQIINQIDLSSY------GYARHFK-----FLKEFKIIL 344        ++     R      YQ+    +   Y      G +   K      +  F+I Sbjct: 302 -------IVWKTFNRFEKNFLYQVATGKEFIEYCTRFATGTSNSHKRVSPDIMVGFQIPF 354 Query: 345 PSKDISQKYNEIANTFFVKVRNNLKQNHHLTQLRDFLLPMLMNGQVSV 392     I QK+ EI ++   +V  N +QN  LTQLRD++LPMLMNGQV V Sbjct: 355 EKTHI-QKFGEIIDSIRTQVLQNNEQNQELTQLRDWILPMLMNGQVKV 401

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 95

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 189> which encodes amino acid sequence <SEQ ID 190; NGS95>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −6.12   Possible cleavage site: 19 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 3  value:  −10.51 threshold:  0.0   INTEGRAL Likelihood = −10.51 Transmembrane 112-128   (109-132)   INTEGRAL Likelihood = −4.46 Transmembrane 50-66 (46-70)   INTEGRAL Likelihood = −2.23 Transmembrane 7-23 (7-23)   PERIPHERAL Likelihood = 4.19   modified ALOM score: 2.60 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----      bacterial inner membrane --- Certainty= 0.520      (Affirmative) < succ>

The protein has homology with the following sequences in the databases: >pir||G69096 hypothetical protein MTH1717-Methanobacterium thermoautotrophicum (strain Delta H) gb|AAB86189.1|(AE000928) unknown [Methanothermobacter thermautotrophicus] Length = 557 Score = 35.4 bits (80), Expect = 0.50 Identities = 25/80 (31%), Positives = 47/80 (58%), Gaps = 5/80 (6%) Query: 52 LLFYFLIPFIATATVLWLSKYLGKDEFKQGEVKELEYVNDNFLPSYLGYFFVALSIPDNN 111 L+F+F+ P + TATVL + K + ++ F++ EV  L     + +PS++     ++ IP++ Sbjct: 92 LVFFFISPLLGTATVLVIYK-VARETFEREEVALLSAFLFSMVPSFVAR--TSVFIPESM 148 Query: 112 LFLLFVMYGIIFLLVSCSKS 131   LL    GI+++LV   K+ Sbjct: 149 GLLL--TSGILYMLVKYLKT 166

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 96

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 191> which encodes amino acid sequence <SEQ ID 192; NGS96>. Analysis of this protein sequence reveals the following: GyH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −7.76   Possible cleavage site: 28 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  6.15 threshold:  0.0   PERIPHERAL Likelihood = 6.15   modified ALOM score: −1.73 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.362(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 97

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 193> which encodes amino acid sequence <SEQ ID 194; NGS97>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)   Signal Score (−7.5): −0.48   Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:  calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0  value:  8.86 threshold:  0.0   PERIPHERAL Likelihood = 8.86   modified ALOM score: −2.27 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty= 0.127(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >ref|NP_052265.1|P2 J homolog; baseplate or base of tail fibre [Enterobacteria phage 186] gb|AAC34162.1|(U32222) P2 J homolog; baseplate or base of tail fibre [Enterobacteria phage 186] Length = 302 Score = 112 bits (280), Expect = 3e−24 Identities = 65/151 (43%), Positives = 85/151 (56%), Gaps = 1/151 (0%) Query: 1 MGNSRLSQLPAPAAIEETDFEGIFARKKAALTALCPESIRETVAQTLELESEPLTIDLQQ 60 M    LS LP P  +EE DFE I A + A L +L PE  +E VA+TL LESEP+   LQ+ Sbjct: 1 MATVDLSLLPVPDVVEELDFETILAERIATLISLYPEDQQEAVARTLALESEPIVKLLQE 60 Query: 61 QAYQELLVRNRINEAVKANLLAYAQGSDLDHIAAQYGLSRKTIRXXXXXXXXXXXXEYET 120  AY+E++ R R+NEA +A +LAYA+ SDLD++ A + + R  +R            E E Sbjct: 61 NAYREVIWRQRVNEAARAGMLAYARDSDLDNLGANFNVERLVVRPADDTTIPPTPAEMEL 120 Query: 121 DDAFRARV-QAHPEKYAAGPRTAYEAHAIDA 150 D  FR R+ QA      AG   AYE H   A Sbjct: 121 DADFRLRIQQAFEGMSVAGSTGAYEFHGRSA 151

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 98

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 195> which encodes amino acid sequence <SEQ ID 196; NGS98>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.68    Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.61 threshold: 0.0    PERIPHERAL Likelihood = 4.61    modified ALOM score: −1.42 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.182(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 99

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 197> which encodes amino acid sequence <SEQ ID 198; NGS99>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −4.87   Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.93 threshold: 0.0    PERIPHERAL Likelihood = 4.93    modified ALOM score: −1.49 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.189(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|10172952|dbj|BAB04058.1|(AP001508) BH0339-unknown conserved protein in others [Bacillus halodurans] Length = 283 Score = 83.7 bits (206), Expect = 1e−15 Identities = 59/156 (37%), Positives = 87/156 (54%), Gaps = 8/156 (5%) Query: 10 VRGPVQLAFAQSIDPIVPPEVSITRMAVTNEKDLEKERTMGRKYIVPYVVYRVHGFISAN 69 VRGPV +  A SIDPI      IT+   +   D     TMG K+ V + VY   G I+ Sbjct: 129 VRGPVSIHTATSIDPIDIVSTQITKSVNSVTGDKRSSDTMGMKHRVDFGVYVFKGSINTQ 188 Query: 70 LAAKTGFSDDDLAKLWQALTLMFEHDRSAAR--GEMARKLVFKHDSALGSQPAHKLFD 127 LA KTGF+++D  K+ +AL +FE+D S+AR  G M   K+  ++H S LG   + K+ Sbjct: 189 LAEKTGFTNEDAEKIKRALITLFENDSSSARPDGSMEVHKVYWWEHSSKLGQYSSAKVHR 248 Query: 128 AVKVERVNGESGTPASGFGDYKISVVSDGLNGVSVE 163 ++K+E    ++ TP S F DY + +    L+G+ VE Sbjct: 249 SLKIE---SKTDTPKS-FDDYAVELYE--LDGLGVE 278

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 100

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 199> which encodes amino acid sequence <SEQ ID 200; NGS100>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.03    Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.63 threshold: 0.0    PERIPHERAL Likelihood = 6.63    modified ALOM score: −1.83 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.185(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|1175791|sp|P44189|YE18_HAEIN HYPOTHETICAL PROTEIN HI1418 gi|1074769|pir||A64029 hypothetical protein HI1418-Haemophilus influenzae (strain Rd KW20) gi|1574254|gb|AAC23068.1|(U32821) H. influenzae predicted coding region HI1418 [Haemophilus influenzae Rd] Length = 201 Score = 144 bits (364), Expect = 1e−33 Identities = 71/109 (65%), Positives = 79/109 (72%) Query: 8 NFQQNSVRTVADNKGELWFLANDVCEILGYTNPRRTVDLHCKSRGVTKRYTPTTSGEQEM 67 NF+   VR + D KGE WF   DVC ILGYTN R+ +  HCK  GVTKRYTPT S +QEM Sbjct: 24 NFKDLPVRVILDPKGEFWFCGTDVCHILGYTNSRKALQDHCKQGGVTKRYTPTKSADQEM 83 Query: 68 TYINEPNLYRLIIKSRKPAAEAFEEWVMETVLPAIRKTGGCQVGPKTTA 116 T+INEPNLYRLIIKSRKP AE FE WV E VLP IRKTG  Q+ P+  A Sbjct: 84 TFINEPNLYRLIIKSEKPEAEPFEAWVFEEVLPQIRKTGKYQLQPQQLA 132

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 101

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 201> which encodes amino acid sequence <SEQ ID 202; NGS101>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −1.23    Possible cleavage site: 47 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.55 threshold: 0.0    PERIPHERAL Likelihood = 3.55    modified ALOM score: −1.21 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.126(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|9632520|ref|NP_049514.1|hypothetical protein [Bacteriophage 933W] gi|9633449|ref|NP_050552.1|hypothetical protein [Bacteriophage VT2-Sa] gi|4585431|gb|AAD25459.1|AF125520_54 (AF125520) hypothetical protein [Bacteriophage 933W] gi|5881645|dbj|BAA84336.1|(AP000363) hypothetical protein [Bacteriophage VT2-Sa] gi|7649882|dbj|BAA94l60.1|(AP000422) hypothetical protein [Escherichia coli O157:H7] Length = 404 Score = 177 bits (449), Expect = 3e−43 Identities = 130/425 (30%), Positives = 204/425 (47%), Gaps = 27/425 (6%) Query: 7 TAYGDPQAMMKQAAGLFAMHMQRNSTLNRLAGKMPAGTA-GAEATLRKQTTQHMPVVRCQ 65 T     QA       LF    +  S +N L  +  A  A   +    KQT+   PVVR Sbjct: 2 TTVTSAQANKLYQVALFTAANRNRSMVNILTEQQEAPKAVSPDKKSTKQTSAGAPVVRIT 61 Query: 66 DLTRGMGDEIRFNLVNPVSALPIMGDNTAEGRGVGMSLSEAGLRVNQARFPVDGGGTMTN 125 DL +  GDE+ F++++ +S  P MGD   EGRG  +S ++  L++NQ R  VD GG M+ Sbjct: 62 DLNKQAGDEVTFSIMHKLSKRPTMGDERVEGRGEDLSHADFSLKINQGRHLVDAGGRMSQ 121 Query: 126 QRSPADYRALIRPAAQSLMDRYADQTLLVHMAGARGFHDNIEWGVPLAGDPKFNDYAVNP 185 QR+  +  +  R    +  +   DQ  +VH+AGARG     +  +P A  P+F    +N Sbjct: 122 QRTKFNLASSARTLLGTYFNDLQDQCAIVHLAGARGDFVADDTILPTAEHPEFKKIMIND 181 Query: 186 VKAPSKNRHFTASGDAVTGVGDNGGELKIASTDLFTMDTVDSMRTVLDQIPLPPPIVKFE 245 V  P+ +RHF          GD     +I + D+F++  VD++   +D++  P   V+ Sbjct: 182 VLPPTHDRHFFG--------GDATSFEQIEAADIFSIGLVDNLSLFIDEMAHPLQPVRLS 233 Query: 246 GDKAAGDSPLRVWLLSPAQYNRF---AADPKFRQLQASAIARASQANQNPLFLGDAGLWN 302 GD+  G+ P  V  ++P Q+N +    +   + Q+   A+ RA   N +PLF G+  +W Sbjct: 234 GDELHGEDPYYVLYVTPRQWNDWYTSTSGKDWNQMMVRAVNRAKGFN-HPLFKGECAMWR 292 Query: 303 GFILVKMP-RPIRFYAGDEMKYCADKFSEAESGLKIPASFADKFAVDRSVILGGQAVLEA 361 ++ K    PIRFY G ++    +  +            A    +DR++++LG QA+  A Sbjct: 293 NILVRKYAGMPIRFYQGSKVLVSENNLTATTK------EVAAATNIDRAMLLGAQALANA 346 Query: 362 FANTGKHGGMPFFWSEKELDHGNRVETLVGTIRGVAKTRFAVDVGGGAKEITDYGVTVVD 421 +   G+  G  F   EK+ D  NR E  +  I G+ K RF    G    ++ D+GV  VD Sbjct: 347 Y---GQKAGGHFNMVEKKTDMDNRTEIAISWINGLKKIRFPEKSG----KMQDHGVIAVD 399 Query: 422 TVVPL 426 T V L Sbjct: 400 TAVKL 404

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 102

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 203> which encodes amino acid sequence <SEQ ID 204; NGS 102>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −6.09    Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.92 threshold: 0.0    PERIPHERAL Likelihood = 2.92    modified ALOM score: −1.08 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.480(Affirmative) < succ

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 103

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 205> which encodes amino acid sequence <SEQ ID 206; NGS 103>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −1.29    Possible cleavage site: 34 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −0.00 threshold: 0.0    INTEGRAL Likelihood = −0.00 Transmembrane    22-38 (22-38)    PERIPHERAL Likelihood = 4.88    modified ALOM score: 0.50 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.100(Affirmative) < succ>

The protein has homology with the following sequences in the databases: >gi|11277848|pir||E81145 replicative DNA helicase NMB0885 [imported]-Neisseria meningitidis (group B strain MD58) gi|7226124|gb|AAF41296.1|(AE002441) replicative DNA helicase [Neisseria meningitidis MC58] Length = 468 Score = 233 bits (594), Expect = 5e−60 Identities = 158/456 (34%), Positives = 245/456 (53%), Gaps = 34/456 (7%) Query: 15 SVGAEQNILGGILIEPTAIARCA-ILTPEKFYQAQHRIIFRALLDMAAANEPIDIITLND 73 S+ AEQ++LGG+++E  A  R A +++ E FY+ +HR+IFR++  +   + P D+IT+ + Sbjct: 23 SMEAEQSVLGGLMLENPAWDRIADVVSGEDFYRHEHRLIFRSIAKLINESRPADVITVQE 82 Query: 74 KLEARGEAENAGGLAYLIDLNQNTPSAKNISRYVGIVNDRFVERGLLKASAAIEKIAVSK 133  L+   E E AGG  YLI L QNTPSA NI RY  IV +R + R L +    I + A + Sbjct: 83 DLQRNEELEAAGGFEYLITLAWNTPSAANIRRYAEIVRERSIMRQLAEVGTEIARSAYNP 142 Query: 134 DGGTVAEKLSKAADELAAVGKDAVKRETKTFGQTVEDLIGGLDKRLDGVR--------FG 185  G    + L +A +++  + +   K  +K     + DL+  + +R+D +          G Sbjct: 143 QGRDAGQLLDEAENKVFQIAESTAK--SKQGFLEMPDLLKEVVQRIDMLYSRDNPDEVTG 200 Query: 186 LPTGLMKLDGMTGGLPDGNLIVIAARPSMGKTVLAENIARFALKQGK-AVHFQSYEMSAV 244 +PTG + LD  T GL  G+LI++A RPSMGKT  + NIA     +G+  V   S EM Sbjct: 201 VPTGFIDLDKKTSGLQPGDLIIVAGRPSMGKTAFSINIAEHVAVEGRLPVAVFSMEMGGA 260 Query: 245 ELARRGMAAECNIPMQNLKTGNLTQSDYANM----------PIYVSQAKEWKFDVNCDLL 294 +L  R + +   +    LKTG L    +  +          P+Y+ + Sbjct: 261 QLVMRMLGSVGRLDQSVLKTGRLEDEHWGRLNEAVVKLSDAPVYIDETPGLTALELRARA 320 Query: 295 NVDELCFLAKEKKLTTGLDLLVVDHLHIMPRAGRDE--VAELGNISRRLKNLAAELNTPV 352       F  K       L L+V+D+L +M  +GR +   +ELG ISR LK LA EL  P+ Sbjct: 321 RRLARQFNNK-------LGLIVIDYLQLMAGSGRSDNRASELGEISRSLKALAKELQVPI 373 Query: 353 VLVAQLNRGNTKQADKRPNMADIRGSGAIEQDANIIIMPHRESYYDGNENP--SIAELII 410 + ++QL+R    + DKRP M+D+R SGAIEQDA++I+  +R+ YY+  ++P   +AE II Sbjct: 374 IALSQLSRTVESRTDKRPMMSDLRESGAIEQDADLIMFLMYRDEYYN-QDSPMKGLAECII 432 Query: 411 AKNRDGEMGTVVCGWKGQFMKFEEEPDLAWQAPKHD 446  K+R+G +G +   W GQF KF+    +  +A   D Sbjct: 433 GKHRNGPVGKIFLTWTGQFTKFDNAAYIPEEAKIED 468 >gi|11277846|pir||E81876 probable replicative DNA helicase (EC 3.6.1.-) NMA1105 [imported]- Neisseria meningitidis (group A strain Z2491) gi|7379799|emb|CAB84367.1|(AL162755) putative replicative DNA helicase [Neisseria meningitidis Z2491] Length = 468 Score = 230 bits (588), Expect = 2e−59 Identities = 158/456 (34%), Positives = 244/456 (52%), Gaps = 34/456 (7%) Query: 15 SVGAEQNILGGILIEPTAIARCA-ILTPEKFYQAQHRIIFRALLDMAAANEPIDIITLND 73 S+ AEQ++LGG+++E  A  R A +++ E FY+ +HR+IFR++  +   + P D+IT+ + Sbjct: 23 SMEAEQSVLGGLMLENPAWDRIADVVSGEDFYRHEHRLIFRSIAKLINESRPADVITVQE 82 Query: 74 KLEARGEAENAGGLAYLIDLNQNTPSAKNISRYVGIVNDRFVERGLLKASAAIEKIAVSK 133  L+   E E AGG  YLI L QNTPSA NI RY IV +R + R L +    I + A + Sbjct: 83 DLQRNEELEAAGGFEYLITLAQNTPSAANIRRYAEIVRERSIMQLAEVGTEIARSAYNP 142 Query: 134 DGGTVAEKLSKAADELAAVGKDAVKRETKTFGQTVEDLIGGLDKRLDGVR--------FG 185  G    + L +A +++  + +   K  +K     + DL+  + +R+D +          G Sbjct: 143 QGRDAGQLLDEAENKVFQIAESTAK--SKQGFLEMPDLLKEVVQRIDMLYSRDNPDEVTG 200 Query: 186 LPTGLMKLDGMTGGLPDGNLIVIAARPSMGKTVLAENIARFALKQGK-AVHFQSYEMSAV 244 + TG + LD  T GL  G+LI++A RPSMGKT  + NIA     +GK  V   S EM Sbjct: 201 VSTGFIDLDKKTSGLQPGDLIIVAGRPSMGKTAFSINIAEHVAVEGKLPVAVFSMEMGGA 260 Query: 245 ELARRGMAAECNIPMQNLKTGNLTQSDYANM----------PIYVSQAKEWKFDVNCDLL 294 +L  R + +   +    LKTG L    +  +          P+Y+ + Sbjct: 261 QLVMRMLGSVGRLDQSVLKTGRLEDEHWGRLNEAVVKLSDAPVYIDETPGLTALELRARA 320 Query: 295 NVDELCFLAKEKKLTTGLDLLVVDHLHIMPRAGRDE--VAELGNISRRLKNLAAELNTPV 352       F  K       L L+V+D+L +M  +GR +   +ELG ISR LK LA EL  P+ Sbjct: 321 RRLARQFNNK-------LGLIVIDYLQLMAGSGRSDNRASELGEISRSLKALAKELQVPI 373 Query: 353 VLVAQLNRGNTKQADKRPNMADIRGSGAIEQDANIIIMPHRESYYDGNENP--SIAELII 410 + ++QL+R    + DKRP M+D+R SGAIEQDA++I+  +R+ YY+ ++P   +AE II Sbjct: 374 IALSQLSRTVESRTDKRPMMSDLRESGAIEQDADLIMFMYRDEYYN-QDSPMKGLAECII 432 Query: 411 AKNRDGEMGTVVCGWKGQFMKFEEEPDLAWQAPKHD 446  K+R+G +G +   W GQF KF+    +  +A   D Sbjct: 433 GKHRNGPVGKIFLTWTGQFTKFDNAAYIPEEAKIED 468

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 104

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 207> which encodes amino acid sequence <SEQ ID 208; NGS104>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −2.11    Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value:  5.04 threshold: 0.0    PERIPHERAL Likelihood = 5.04    modified ALOM score: −1.51 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.220(Affirmative) < succ

The protein has homology with the following sequences in the databases: >gi|7515458|pir||T13296 hypothetical protein 8-Streptococcus phage phi- O1205 gi|2444088|gb|AAC79524.1|(U88974) ORF8 [Streptococcus thermophilus temperate bacteriophage O1205] Length = 157 Score = 62.1 bits (150), Expect = 3e−09 Identities = 53/161 (32%), Positives = 86/161 (52%), Gaps = 8/161 (4%) Query: 5 TLYRCAADVQAGLDYYFDSETEREDTLEAV--IGQFEVKAQSVIAYIKNQEITEKMLEGH 62 TLY     +    +   D ET + DTLEA+     +E K +  +  IK+ E   +  + Sbjct: 3 TLYELTDQLLEIYNMDVDDET-KLDTLEAIDWTTDYENKVEGYVKVIKSLEADIEARKNE 61 Query: 63 IRQMTGKLKAAKARNQSLKDYLARNMQAAGITEIKADDGTFKASFRKSEAVVILDEAQIP 122  +++ G  K+ +++   LK  LA +M   G T +  D  FK  FRKSEAVV+ +E ++P Sbjct: 62 KKRLDGLNKSDQSKIDKLKTALAVSMAETGQTRV--DTTLFKVGFRKSEAVVV-NEEEKLP 118 Query: 123 AEFMREAVKTEPDKTAIRKAIESGRQVAGAKIEGRKNLQIR 163  E+     K  PDK  +++ ++SG+ + GA +E R+NL IR Sbjct: 119 KEYQIATYK--PDKKTLKBLLKSGKHIEGATLEERRNLNIR 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 105

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 209> which encodes amino acid sequence <SEQ ID 210; NGS 105>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −5.52    Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.60 threshold: 0.0    PERIPHERAL Likelihood = 2.60    modified ALOM score: −1.02 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.135(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 106

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 211> which encodes amino acid sequence <SEQ ID 212; NGS 106>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): 4.8    Possible cleavage site: 26 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 27 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value:  7.80 threshold: 0.0    PERIPHERAL Likelihood = 7.80    modified ALOM score: −2.06 Score for OM-PP discrimination: 4.38 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 4.38 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane? Score: 0.437687 Outer membrane? Score: 0.437687 ----- Final Results -----     bacterial outer membrane --- Certainty=     0.768(Affirmative) < succ>

The protein has no homology with sequences in the databases, although it is similar to HMW1 from Haemophilus influenzae.

The protein was expressed in E.coli as an insoluble 43.56 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 107

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 213> which encodes amino acid sequence <SEQ ID 214; NGS 107>. Analysis of this protein sequence reveals the following: Signal Score (−7.5): −3.83    Possible cleavage site: 51 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.61 threshold: 0.0    PERIPHERAL Likelihood = 4.61    modified ALOM score: −1.42 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.146(Affirmative) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 108

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 215> which encodes amino acid sequence <SEQ ID 216; NGS108>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne) Signal Score (−7.5): −6.14    Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 8.43 threshold: 0.0    PERIPHERAL Likelihood = 8.43    modified ALOM score: −2.19 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.574(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||G81977 probable lipoprotein NMA0586 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB83877.1|(AL162753) putative lipoprotein [Neisseria meningitidis Z2491] Length = 280 Score = 52.9 bits (126), Expect = 5e−06 Identities = 43/134 (32%), Positives = 63/134 (46%), Gaps = 23/134 (17%) Query: 174 LGDIRGVATDEDKLPKAGSFQYEGRAFGGNGVLSKESLDNHNGVFRYTIDFDRRKGSGSI 233 +GDI G  T  DKLP+ G   Y G AFG          D+ +G   YTIDF  ++G G I Sbjct: 156 IGDIAGEHTSFDKLPEGGRATYRGTAFGS---------DDASGKLTYTIDFAAKQGHGKI 206 Query: 234 EGMEQYGKIKLEEAAIERIPYRESGSSLGLKDRVSYFGVNEGVAMLEKDNEIKKYHLGIF 293 E ++   ++ ++ AA +  P ++ + +               ++L    E   Y LGIF Sbjct: 207 EHLKS-PELNVDLAASDIKPDKKRHAVI-------------SGSVLYNQAEKGSYSLGIF 252 Query: 294 GEAANEVAGAVSQE 307 G  A EVAG+   E Sbjct: 253 GGQAQEVAGSAEVE 266 >pir||D81032 hypothetical protein NMB1870 [imported]-Neisseria meningitidis (group B strain MD58) gb|AAF42204.1|(AE002537) hypothetical protein [Neisseria meningitidis MC58] Length = 320 Score = 50.6 bits (120), Expect = 3e−05 Identities = 50/168 (29%), Positives 76/168 (44%), Gaps = 28/168 (16%) Query: 136 VYEQPYSVVRGYFGYSRKDGNPIEGDGQNPEEIPFDLYLGDIRGVATDEDKLPKAGSFQY 195 VY+Q +S +  +     +D    E  G+   +  F   +GDI G  T  DKLP+ G   Y Sbjct: 163 VYKQSHSALTAFQTEQIQDS---EHSGKMVAKRQFR--IGDIAGEHTSFDKLPEGGRATY 217 Query: 196 EGRAFGGNGVLSKESLDNHNGVFRYTIDFDRRKGSGSIEGMEQYGKIKLEEAAIERIPYR 255  G AFG          D+  G   YTIDF  ++G+G IE ++   ++ ++ AA +  P Sbjct: 218 RGTAFGS---------DDAGGKLTYTIDFAAKQGNGKIEHLKS-PELNVDLAAADIKPDG 267 Query: 256 ESGSSLGLKDRVSYFGVNEGVAMLEKDNEIKKYHLGIFGEAANEVAGA 303 +  + +              ++L    E   Y LGIFG  A EVAG+ Sbjct: 268 KRHAVI-------------SGSVLYNQAEKGSYSLGIFGGKAQEVAGS 302

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 109

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 217> which encodes amino acid sequence <SEQ ID 218; NGS109>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.39    Possible cleavage site: 25 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.00 threshold: 0.0    PERIPHERAL Likelihood = 7.00    modified ALOM score: −1.90 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.353(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >pir||A82012 hypothetical protein NMA0179 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB83494.1|(AL162752) hypothetical protein NMA0179 [Neisseria meningitidis Z2491] Length = 97 Score = 183 bits (464), Expect = 1e−45 Identities = 92/97 (94%), Positives = 95/97 (97%) Query: 44 MKANDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVSIHNRKADYAEKGKERIALF 103 MK NDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVS+HNRKADYAEKGKE+IALF Sbjct: 1 MKTNDKLNRQIDVLQKQSAAIHNEAYIEMNTLLYRHREVVSVHNRKADYAEKGKEQIALF 60 Query: 104 PRGLNGITKLPAAVLLPERPYHFDMKEVLYIFSRIPR 140 PRGLNGITKLPAAVLLPERPYHFDMKEVL+IFS IPR Sbjct: 61 PRGLNGITKLPAAVLLPERPYHFDMKEVLHIFSWIPR 97

As a homolog was found in serogroup A N.meningitidis but not in serogroup B, NGS109 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 110

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 219> which encodes amino acid sequence <SEQ ID 220; NGS110>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −2.76    Possible cleavage site: 41 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −0.00 threshold: 0.0    INTEGRAL Likelihood = −0.00 Transmembrane    88-104 (88-104)    PERIPHERAL Likelihood = 7.69    modified ALOM score: 0.50 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.100(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology with sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 111

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 221> which encodes amino acid sequence <SEQ ID 222; NGS111>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.89    Possible cleavage site: 21 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.44 threshold: 0.0    PERIPHERAL Likelihood = 2.44    modified ALOM score: −0.99 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.293(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology with the following sequences in the databases: >gb|AAC45840.1|(AF001598) restriction endonuclease [Neisseria gonorrhoeae] Length = 374 Score = 539 bits (1390), Expect = e−152 Identities = 285/285 (100%), Positives = 285/285 (100%) Query: 1 MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT 60 MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT Sbjct: 90 MGFIEPFLSSYTPLSRDYVQARTNRKRQTLLSKIVYTHSGFQRSVTENSNIRQINFLIKT 149 Query: 61 LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN 120 LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN Sbjct: 150 LVEHPQGKLNKKEIAAMMLVDLKTFQQDYLTETELNDYFQQGIESGFIERKYNQISYLWN 209 Query: 121 LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK 180 LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK Sbjct: 210 LLDKLDDLKRVGDDLYFAEDAQRIFGNLDEITVRKRDPYLHRLYKNQLQEESEEHYGNVK 269 Query: 181 CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS 240 CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS Sbjct: 270 CMLEKLAYPVLIASHIKPFILSDDTEAYDPNNGLLLSRTLDSLFDLKYISFDDEGNMVKS 329 Query: 241 KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI 285 KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI Sbjct: 330 KRLSDDVWRRWCDVKLDNNLLNDKRKSYLAYHRELMLQEDQEFHI 374

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 112

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 223> which encodes amino acid sequence <SEQ ID 224; NGS112>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −9.08    Possible cleavage site: 54 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −1.22 threshold: 0.0    INTEGRAL Likelihood = −1.22 Transmembrane    160-176 (160-177)    PERIPHERAL Likelihood = 0.58    modified ALOM score: 0.74 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.149(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_12644572 gi|12644572|sp|Q50973|T2B1_NEIGO TYPE II RESTRICTION ENZYME NGOBI (ENDONUCLEASE NGOBI) (R.NGOBI) (R.NGOI) gb|AAB03207.2|(U42459) NgoI restriction endonuclease R.NgoI [N. gonorrhoeae] Length = 350 Score = 694 bits (1791), Expect = 0.0 Identities = 349/350 (99%), Positives = 349/350 (99%) Query: 1 MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE 60 MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE Sbjct: 1 MTLEEQQAKEALDGIIKKSRVHLYKPIQIAEILYHDRCIKQLDFLNLDTYRNQSKRWRDE 60 Query: 61 ICRRFLGISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESTITKQFFNRFSQM 120 ICRRFLGISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESTITKQFFNRFSQM Sbjct: 61 ICRRFLGISTSSAKFQDNLFEKNAIPPEKLAVLGTLNRQSDGGVESTITKQFFNRFSQM 120 Query: 121 SEALAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID 180 SEALAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID Sbjct: 121 SEALAYVGNTDRYSFQLSEFLNLFWLEPGLKRSIDKIYEIVVYALFDALVSELGITVSID 180 Query: 181 FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK 240 FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK Sbjct: 181 FPKENLFLWEEYQDFAEKIITMPKNEHLKLPAKIHRVGVTNAADRGLDMWSNFGLAIQVK 240 Query: 241 HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE 300 HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE Sbjct: 241 HLSLDEELAEDIVSSISADRIVIVCKKAEQSVIVSLLTQIGWKSRIQNIVTEDDLISWYE 300 Query: 301 KALRQQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF 350 KALRQQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF Sbjct: 301 KALRQQYPIAEALLENIKTEIMREFPAVNEANEFLDFAQNRGYDITVTHF 350

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 113

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 225> which encodes amino acid sequence <SEQ ID 226; NGS113>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −1.7    Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 4 value: −9.77 threshold: 0.0    INTEGRAL Likelihood = −9.77 Transmembrane    187-203 (183-208)    INTEGRAL Likelihood = −7.22 Transmembrane     25-41 (19-46)    INTEGRAL Likelihood = −4.14 Transmembrane    139-155 (138-155)    INTEGRAL Likelihood = −2.87 Transmembrane     86-102 (85-102)    PERIPHERAL Likelihood = 1.27    modified ALOM score: 2.45 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.491(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15902668 gi|15902668|ref|NP_358218.1|\(NC_003098) ABC transporter membrane-spanning permease-glutamine transport [Streptococcus pneumoniae R6] gb|AAK99428.1|(AE008440) ABC transporter membrane-spanning permease- glutamine transport [Streptococcus pneumoniae R6] Length = 226 Score = 218 bits (556), Expect = 7e−56 Identities = 113/218 (51%), Positives = 155/218 (70%) Query: 1 MNWPYLIDAVPKFADAAKLTLELSVYGVVLSLLFLPVAVVTAYRIRPFYALARAYIELS 60 M+W  +   +P +  A  LTL ++V+G++ S L GL V+++  YRI     +A AYIEILS Sbjct: 1 MNWPYLIDAVPKFADAAKLTLELSVYGVVLSLLFGLPVAVVTAYRIRPFYALARAYIELS 60 RNTPLLIQLFFLY+GLP++GI      C  + LVFLG SYMAE+ R+G+ A+ + Q   G Query: 61 RNTPLLIQLFFLYYGLPKMGIKWDGFTCGVIALVFLGASYMAEAVRAGILAVPKGQVGAG 120 RNTPLLIQLFFLY+GLP++GI      C  +LVFLG SYMAE+ R+G+ A+ + G   G Sbjct: 61 RNTPLLIQLFFLYFGLPRIGIVLSSEVCATLGLVFLGGSYMAESFRSGLEAISQTQQEIG 120 Query: 121 KAIGLSRFQVFRYVELPQVWAVAVPAIGANILFLMKETSVVSTVGIAELLFVTKDVIGMD 180  AIGL+  QVFRYV LPQ  AVA+P+  AN++FL+KETSV S V +A+L++V KD+IG+ Sbjct: 121 LAIGLTPLQVFRYVVLPQATAVALPSFSANVIFLIKETSVFSAVALADLMYVAKDLIGLY 180 Query: 181 YKTNEALFLLFAAYLIILLPVSLLARRIENRVRSAKYG 218 Y+T+ AL +L  AYLI+LLP+SL+   IE R+R A +G Sbjct: 181 YETDIALAMLVVAYLIMLLPISLVFSWIERRIRHAGFG 218

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 114

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 227> which encodes amino acid sequence <SEQ ID 228; NGS 114>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.46    Possible cleavage site: 17 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 18 ALOM: Finding transmembrane regions (Klein et al.)    count: 3 value: −5.36 threshold: 0.0    INTEGRAL Likelihood = −5.36 Transmembrane     50-66 (47-67)    INTEGRAL Likelihood = −4.83 Transmembrane    183-199 (176-200)    INTEGRAL Likelihood = −1.81 Transmembrane     72-88 (72-88)    PERIPHERAL Likelihood = 0.26    modified ALOM score: 1.57 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.314(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15902667 gi|15902667|ref|NP_358217.1|\(NC_003098) ABC transporter membrane-spanning permease-glutamine transport [Streptococcus pneumoniae R6] gb|AAK99427.1|(AE008440) ABC transporter membrane-spanning permease- glutamine transport [Streptococcus pneumoniae R6] Length = 225 Score = 218 bits (555), Expect = 9e−56 Identities = 111/206 (53%), Positives = 151/206 (72%) Query: 3 EGLLLTAQISLISVAASCVLGTLFGLVLRSRNRLVRFVGRFYLETIRIVPILVWLFGLYF 62 +GL +T  IS++SV  S + GT+ G+++ S +R++RF+ R YLE  IRI+P LV LF +YF Sbjct: 20 QGLGVTIGISILSVLLSMMFGTVMGIIMTSHSRIIRFLTRLYLEFIRIMPQLVLLFIVYF 79 Query: 63 GLSVWTGIHIGGFWVCVWVFSLWGVAEMGKLVRGALESIEKHQVESGLAPGLSRGQVFRC 122 GL+    I+I G    + VF+LWG AEMGDLVRGA+ S+ KHQ ESG A GL+  Q++ Sbjct: 80 GLARNFNINISGETSAIIVFTLWGTAEMGDLVRGAITSLPKHQFESGQALGLTNVQLYYH 139 Query: 123 IELPQSIRRVLPGAVNLFTRMIKTSSLAWLIGVIEVVKVGQQIIENSLLTQPNASFWVYG 182 I +PQ +RR+LP A+NL TRMIKT+SL  LIGV+EV KVGQQII+++ LT P ASFW+YG Sbjct: 140 IIIPQVLRRLLPQAINLVTRMIKTTSLVVLIGVVEVTKVGQQIIDSNRLTIPTASFWIYG 199 Query: 183 LIFMLYFFCCWPLSLLAAKLEQKWEH 208  I +LYF  C+P+S L+  LE+ W + Sbjct: 200 TILVLYFAVCYPISKLSTHLEKHWRN 225

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 115

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 229> which encodes amino acid sequence <SEQ ID 230; NGS 115>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.639999    Possible cleavage site: 38 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:   calculated from 23 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 5.25 threshold: 0.0    PERIPHERAL Likelihood = 5.25    modified ALOM score: −1.55 Rule: inner or outer membrane protein Rule: inner or outer membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----     bacterial outer membrane --- Certainty=     0.790(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.700(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_4588485 gi|4588485|gb|AAD26123.1|\(AF109148) antigenic protein [Actinobacillus pleuropneumoniae] Length = 278 Score = 407 bits (1045), Expect = e−112 Identities = 212/282 (75%), Positives = 242/282 (85%), Gaps = 7/282 (2%) Query: 1 MKLNAKLKALLASAAIAVGLTACGGGSGDAQSSQSSGAA-TVAAIKEKGVIRIGVFGDKP 59 MKL+  LK LLA+A  A  LTAC     +A ++QSS A  +VA IKEKGVIRIGVFGDKP Sbjct: 1 MKLSTTLKTLLATAITAFALTACD----NANNAQSSTAKDSVAQIKEKGVIRIGVFGDKP 56 Query: 60 PFGYVDANGKNQGFDVEIAKDLAKDLLGSPDKVEFVLTEAANRVEYVRSGKVDLILANFT 119 PFGYVDANGK+QGFDVEIAK++A DLLGS DKVEFVLTEAANRVEY++S KVDLILANFT Sbjct: 57 PFGYVDANGKSQGFDVEIAKEIANDLLGSSDKVEFVLTEAANRVEYLKSNKVDLILANFT 116 Query: 120 QTPERAEAVDFADPYMKVALGVVSPKNKPITDMAQLKDQTLLVNKGTTADAFFTKSHPEV 179 +TPERAE VDFA PYM VALGVVSPK + I+D+ QL+ +TLLVNKGTTADA+FTK+HPE+ Sbjct: 117 KTPERAEVVDFAAPYMNVALGVVSPKVRLISDLKQLEGKTLLVNKGTTADAYFTKNHPEI 176 Query: 180 KLLKFDQNTETFDALKDGRGVALAHDNALLWAWAKENPNFEVAIGNLGPAEFIAPAVQKG 239  LLKFDQNTETFDALKDGRGVALAHDNAL+WAWAKENP F+VAIG++GPAE IAPVQKG Sbjct: 177 NLLKFDQNTETFDALKDGRGVALAHDNALVWAWAKENTFDVAIGSVGPAEQIAPAVQKG 236 Query: 240 NADLLNWVNGEIAAMKKDGRLKAAYEKTLLPVYGEKVKPEAL 281 N  LL+ +N EIA  K +G+LKAAYEKTL+PVYG+  KPE L Sbjct: 237 NQALLDVINKEIAEFKTNGKLKAAYERKTLVPVYGD--KPELL 276

The protein was expressed in E.coli as a soluble 28.16 kDa His-fusion product, lacking its leader peptide and its poly-glycine sequence (GGGSG), and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 116

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 231> which encodes amino acid sequence <SEQ ID 232; NGS116>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −7.13    Possible cleavage site: 61 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −1.86 threshold: 0.0    INTEGRAL Likelihood = −1.86 Transmembrane    51-67 (51-67)    PERIPHERAL Likelihood = 1.54    modified ALOM score: 0.87 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.174(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 117

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 233> which encodes amino acid sequence <SEQ ID 234; NGS117>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.25    Possible cleavage site: 40 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 41 ALOM: Finding transmembrane regions (Klein et al.)    count: 2 value: −4.57 threshold: 0.0    INTEGRAL Likelihood = −4.57 Transmembrane    100-116 (99-118)    INTEGRAL Likelihood = −1.59 Transmembrane     54-70 (54-70)    PERIPHERAL Likelihood = 0.53    modified ALOM score: 1.41 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.283(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15793413 gi|15793413|ref|NP_283235.1|\(NC_003116) putative integral membrane protein [Neisseria meningitidis Z2491] pir||C81957 probable integral membrane protein NMA0408 [imported]- Neisseria meningitidis (group A strain Z2491) emb|CAB83707.1|(AL162753) putative integral membrane protein [Neisseria meningitidis Z2491] Length = 550 Score = 1115 bits (2885), Expect = 0.0 Identities = 539/550 (98%), Positives = 545/550 (99%) Query: 1 MVAYAFLFLFVTAAVLLIVRSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV 60 MVAY FLFLFVTAA++LI+RSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV Sbjct: 1 MVAYVFLFLFVTAALVLIIRSHYRWTYFFASALFVFLAGGMLMLTAQWQRALNFASVWFV 60 Query: 61 VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALAGYAVFGWSG 120 VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALA YAVFGWSG Sbjct: 61 VLILFHRLKIHYYKQPLLISDFLLIADWRNWETLFHYKEAVIGMAGLLALAAYAVFGWSG 120 Query: 121 ADSLGMPWRWAGAVLFAAAFVSVRHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF 180 ADSL +PWRWAGAVLFAAAFVS+RHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF Sbjct: 121 ADSLDVPWRWAGAVLFAAAFVSMRHFSKHPGAVKTWLDSLPDDGRDVFLNLPMSCRAVFF 180 Query: 181 QVPVFEGDGEAFARQMPSETRPYGMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG 240 QVPVFEGDGEAFARQMPSETRP GMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG Sbjct: 181 QVPVFEGDGEAFARQMPSETRPCGMSDEKPDIVVTLMESTLDPHCFDFAAAKIPDLKMFG 240 Query: 241 RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR 300 RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR Sbjct: 241 RQEDTVFSSPLRVHTFGGATWKSEFAFLAGVPSTDFGALASGVFYSVVPHLQTGFVRNLR 300 Query: 301 EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR 360 EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR Sbjct: 301 EHGYFCVALSPFTKGNYNAKAAYDHFGFNLMFQPQDLGYPAPMGKNLWHISSEEMMQYAR 360 Query: 361 MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI 420 MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI Sbjct: 361 MILEKRHPDLENVRQPMFVYVLTMKEHGPYRTDTDNVFDLDAPDLNAKTVSALNDYIGRI 420 Query: 421 ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA 480 ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA Sbjct: 421 ADLDKAVESFDRYLHERGKPFVFGYFGDHQVPFEGVSVRKKWDYAQPDYVTQFAVRSNIA 480 Query: 481 GGFVQRQDFLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPNRELVGNYRN 540 GGFVQRQ+FLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPN ELVGNYRN Sbjct: 481 GGFVQRQNFLDLAFAGGVLMEAAGLEAKDGFMRANMAMRGLCGGGLEDCPNWELVGNYRN 540 Query: 541 YLYDVLKIAR 550 YLYDVLKIAR Sbjct: 541 YLYDVLKIAR 550

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS117 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 118

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 235> which encodes amino acid sequence <SEQ ID 236; NGS118>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): 0.59    Possible cleavage site: 19 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:   calculated from 22 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 8.33 threshold: 0.0    PERIPHERAL Likelihood = 8.33    modified ALOM score: −2.17 Rule: inner or outer membrane protein Rule: inner or outer membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----     bacterial outer membrane --- Certainty=     0.790(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.700(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>      bacterial cytoplasm --- Certainty=      0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

The protein was expressed in E.coli as a soluble 12.98 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 119

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 237> which encodes amino acid sequence <SEQ ID 238; NGS119>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.75    Possible cleavage site: 47 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.69 threshold: 0.0    PERIPHERAL Likelihood = 7.69    modified ALOM score: −2.04 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.213(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_2625122 gi|2625122|gb|AAB86635.1|\(AF031495) putative hemoglobin receptor component precursor HpuA [Neisseria gonorrhoeae] Length = 360 Score = 668 bits (1724), Expect = 0.0 Identities = 331/331 (100%), Positives = 331/331 (100%) Query: 1 VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR 60 VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR Sbjct: 30 VSIPTATPLPAGEVTLSSDNGNIENINTAGAGSASDAPSRSRRSLDAAPQNTSGISIRQR 89 Query: 61 EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPKFKIPDRHAGQRLADGSR 120 EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPKFKIPDRHAGQRLADGSR Sbjct: 90 EVEKDYFGYKSKETSFIFKTPGGAQYALSSYADPITVSYSSPKFKIPDRHAGQRLADGSR 149 Query: 121 IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET 180 IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET Sbjct: 150 IFICCSDSGATSYAEITKQDYMKFGAWIGPNGEIDLFAGGFPVGKTPPPAFSYGSSTPET 209 Query: 181 ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVSFITANFNSNTLAGKI 240 ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVSFITANFNSNTLAGKI Sbjct: 210 ALSKGKITYQVWGIRVRNGQFVTSSYTPPKSGSYYGTLANTPVSFITANFNSNTLAGKI 269 Query: 241 LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD 300 LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD Sbjct: 270 LGNSDYGPDVDIQNATITGPTFSGDATSGGKSGKLEGKFFGKFASTRSSEVSIGGKITFD 329 Query: 301 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQ 331 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQ Sbjct: 330 GDRSLDTVFGGVSYEKKLDDTSQDTNHLTKQ 360

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 120

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 239> which encodes amino acid sequence <SEQ ID 240; NGS120>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −7.24    Possible cleavage site: 38 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.42 threshold: 0.0    PERIPHERAL Likelihood = 6.42    modified ALOM score: −1.78 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.280(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gsa_AAR91313 N. gonorrhoeae glycosyltransferase LgtC |WO9610086-A1|09-JUL-1996 Length = 306 Score = 535 bits (1379), Expect = e−151 Identities = 252/253 (99%), Positives = 252/253 (99%) Query: 8 GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP 67 GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP Sbjct: 54 GGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDTDVLVRDGLKP 113 Query: 68 LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC 127 LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC Sbjct: 114 LWDTDLGGNWVGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSC 173 Query: 128 EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT 187 EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT Sbjct: 174 EWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANGFASRHTDPLYLDRT 233 Query: 188 NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTKRMLQRW 247 NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTKRMLQRW Sbjct: 234 NTAMPVAVSHYCGSAKPWHRDCTVWGAERFTELAGSLTTVPEEWRGKLAVPPTKRMLQRW 293 Query: 248 RKKLSARFLRKIY 260 RKKLSARFLRKIY Sbjct: 294 RKKLSARFLRKIY 306

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 121

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 241> which encodes amino acid sequence <SEQ ID 242; NGS121>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.22    Possible cleavage site: 37 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.23 threshold: 0.0    PERIPHERAL Likelihood = 3.23    modified ALOM score: −1.15 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----      bacterial cytoplasm --- Certainty=      0.402(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15281345 gi|15281345|dbj|BAB63435.1|\(AB058945) DNA adenine methylase M.Ssu4109IB [Streptococcus suis] Length = 271 Score = 269 bits (687), Expect = 4e−71 Identities = 127/211 (60%), Positives = 158/211 (74%), Gaps = 1/211 (0%) Query: 1 MIFADPPYFLSNDGFSCQNGQMVSVNKGNWDKSKGMAADLEFYEEWLRLCYALLKPNGTI 60 MIFADPPYFLSN G S   GQ+VSV+KG+WDK   +    EF  +W+RL   +LKPNGTI Sbjct: 44 MIFADPPYFLSNGGISNSGGQVVSVDKGDWDKVNSLEEKHEFNRKWIRLAKNVLKPNGTI 103 Query: 61 WVCGTFHNIYLIGYLMQTVGYHILNNITWEKPNPPPNLSCRFFTHSTETILWAKK-NKKA 119 W+ G+FHNIY +G  ++  G+ ILNNITW+K NP PNLSCR+FTHSTETILWA+K +KKA Sbjct: 104 WISGSFHNIYSVGMALEQEGFKILNNITWQKTNPAPNLSCRYFTHSTETILWARKDDKKA 163 Query: 120 KHTFHYEMMKAQNNGKQMKCVWTFAPPNKTEKTFGKHPTQKPLPLLERCILSASNIGDLI 179 +H ++YE+MK  N+GKQMK VW      K+EK  GKHPTQKP  LLER IL+++  GD I Sbjct: 164 RHYYNYELMKELNDGKQMKDVWVGGLTKKSEKWAGKHPTQKPEYLLERIILASTREGDYI 223 Query: 180 FDPFMGSGTTGVAALKHGRRFCGCELEEDFL 210  DPF+GSGTTGV A + GR+F G + E D+L Sbjct: 224 LDPFVGSGTTGVVAKRLGRKFIGIDAERDYL 254

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 122

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 243> which encodes amino acid sequence <SEQ ID 244; NGS122>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −2.55   Possible cleavage site: 23 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:   calculated from 15 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 11.46 threshold:  0.0   PERIPHERAL Likelihood = 11.46    modified ALOM score: −2.79 Rule: inner or outer membrane protein Rule: inner or outer membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----     bacterial outer membrane --- Certainty= 0.790(Affirmative)     < succ>     bacterial inner membrane --- Certainty= 0.700(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases:

The protein was expressed in E.coli as an insoluble 14.85 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 123

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 245> which encodes amino acid sequence <SEQ ID 246; NGS123>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −5.65   Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 4.24 threshold:  0.0   PERIPHERAL Likelihood = 4.24    modified ALOM score: −1.35 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.404(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to the sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 124

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 247> which encodes amino acid sequence <SEQ ID 248; NGS124>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −5   Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1 value: −1.59 threshold:  0.0   INTEGRAL Likelihood = −1.59 Transmembrane 289-305 (289-305)   PERIPHERAL Likelihood = 3.76    modified ALOM score: 0.82 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.164(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear)       < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_1617515 gi|1617515|gb|AAC82509.1|\(U365994) pilin gene inverting protein homolog PivNG [Neisseria gonorrhoeae] Length = 320 Score = 614 bits (1584), Expect = e−175 Identities = 311/320 (97%), Positivies = 316/320 (98%) Query: 1 MRNTVGLDISKLTFDATAMVGKTEHSAKFDNDSKGLDQFSDRLKSLGYQNLHICMEATGS 60 MRN VGLDISKLTF+A+AMVGKTEHSAKFDNDSKGLDQFSDRLKSLG QNLHICMEATG+ Sbjct: 1 MRNAVGLDISKLTFNASAMVGKTEHSAKFDNDSKGLDQFSDRLKSLGCQNLHICMEATGS 60 Query: 61 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRSAQESELVKRQ 120 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCR A+ESELVKRQ Sbjct: 61 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRLAKESELVKRQ 120 Query: 121 KPTDEQYRLSRMTAAYAKIKSECAAMKNRHHAAKDEEAAKAYAEIIKAMNEQLEVLKEKI 180 KPTDEQYRL RMTAAYAKIKSECAAMKNRHHAAKDEEAAKAYA+IIKAMNEQLEVLKEKI Sbjct: 121 KPTDEQYRLLRMTAAYAKIKSECAAMKNRHHAAKDEEAAKAYAQIIKAMNEQLEVLKEKI 180 Query: 181 KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT 240 KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT Sbjct: 181 KEQTEKPNCKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKESGT 240 Query: 241 SVRGKGKLTKFGNRKLRAVLFMPAMVAVYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV 300 SVRGKGKLTKFGNRKLRAVLFMPAMVAVYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV Sbjct: 241 SVRGKGKLTKFGNRKLRAVLFMPAMVAVYRIRAFPDFIKRLEEKKKPKKVIIAALMRKLAV 300 Query: 301 IAYHVHKKGGDYDPSRYKSA 320 IAYHVHKKGGDYDPSRYKSA Sbjct: 301 IAYHVHKKGGDYDPSRYKSA 320

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 125

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 249> which encodes amino acid sequence <SEQ ID 250; NGS127>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −5.8   Possible cleavage site: 52 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 1.70 threshold:  0.0   PERIPHERAL Likelihood = 1.70    modified ALOM score: −0.84 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.383(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_1076012 gi|1076012|pir||B55225 stress-sensitive restriction system protein 2-Corynebacterium glutamicum (ATCC 13032) gb|AAC00044.1|(U13922) This orf may encode a typeI or typeIII restriction endonuclease which is stress-sensitive and ATP-dependent. It contains a typical ATP binding region (Walker motif) [Corynebacterium glutamicum] Length = 632 Score = 298 bits (764), Expect = 2e−79 Identities = 199/633 (31%), Positives = 321/633 (50%), Gaps = 32/633 (5%) Query: 2 LRTYLNQLTP-PELADSVKNTVDGFMEKLSQTEPKIA-QNVLLLGNVQSGKTAQVLGVLS 59 L Y  +   +L + V  TVD F   +      I+ Q VLL G+VQSGKT+ +LG++++ Sbjct: 7 LNNYITSLSDNADLREKVTATVDAFRHTVMDDFDYISDQQVLLYGDVQSGKTSHMLGIIA 66 Query: 60 ALADDGDHKVFLYLTTDSVDLQDQTVKRAKANLKNFIVLSEADDRSFMEVMKAENP--IL 117    D   H + + LT+ +  L  QT  R      + +V        F    K+  P   + Sbjct: 67 DCLDSTFHTIVI-LTSPNTRLVQQTYDRVAQAFPDTLVCDRDGYNDFRANQKSLTPRKSI 125 Query: 118 VVIKKNARVLKRWRNLFASQSSLKGYPLVIVDDEADAASLNTNSDKPKDASTINKLLND 177 VV+ K   VL  W  +F    +L G+P++I+DDEADA SLNT  ++   D STIN  L Sbjct: 126 VVVGKIPAVLGNWLRVFNDSGALSGHPVLIIDDEADATSLNTKVNQ--SDVSTINHQLTS 183 Query: 178 IKNSCCQSLPIQLTATPQSLLLQHEESDWQPEFIHFFEAGEKYIGGNFVFSDPPS-YIVR 236 I++     +++Q+T TPQ++LLQ ++S+W  E +  F  GE YIGG   FS+  + Y+ Sbjct: 184 IRDLATGCIYLQVTGTPQAVLLQSDDSNWAAEHVLHFAPGESYIGGQLFFSELNNPYLRL 243 Query: 237 FIDSELDDMKDESGEIAEGAKQALLSFLITCAEFALCDKANCNFALHPSYKIQDHQAFSK 296 F +++ D+    S         A+ ++L+T A F L  ++ C   +HPS+    H+ F++ Sbjct: 244 FANTQFDEDSRFS--------DAIYTYLLTAALFLRGESLCTMLIHPSHTASSHRDFAQ 295 Query: 297 KIQAFLNDLVQAVNNGEDLAGSFKESYLDLQKTKPDIHHFDEIYEKLTALLENKQISTLV 356 + +  L    +       +  +F+ +Y  L +T  ++    +I   L  + ++ I   + Sbjct: 296 EARLQLTFAFERFYEPM-IQHNFQRAYEQLAQTDSNLPPLRKILNILGGMEDDFSIH--I 352 Query: 357 VNSQTET-DFDLEKGFNIIIGGNVIGRGLTIPKLQTVYYSRTAKKPNADTFWQHRIFGY 415 VNS   T + D   G+NII+GGN +GRGLT   LQTV+Y R +K+P ADT WQH+R+FGY Sbjct: 353 VNSDNPTVEEDWADGYNIIVGGNSLGRGLTFNNLQTVFYVRESKRPQADTLWQHARMFGY 412 Query: 416 DRDKSLLRLYIPFDVYYFFVQLNQANNLIIGQAKNSG--GNIQVIYPKNINPTRKNVLKF 473  R K  +R+++P  +   F ++   N  I  Q  +     +I+VI    + PTR NVL Sbjct: 413 KRHKDTMRVFMPATIAQTFQEVYLGNEAIKNQLDHGTHINDIRVILGDGVAPTRANVLDK 472 Query: 474 DSINQIVGGVNYFPLHPNEDNLSEINKILPSILKDEIQSDLYQIDIEDLFLVLDKLGRYV 533   +  + GGVNYF   P   N+  ++K L + L    +     I +  +  +L+ Sbjct: 473 RKVGNLSGGVNYFAADPRIIKNVEALDKKLLAYLDKHGEDS--TIGMRAIITILNAF-TVD 529 Query: 534 PDDWNKEKFIAGVEALKAQRPSFKTYVLIKTGRKLSRATGTMLSEDDRKLGEKYPNDLFL 593 P+D +   F A +   +  +P     ++++T RK+++ TG +LS  D+ L         L Sbjct: 530 PNDLDLATFKAALLDFERNQPHLTARMVLRTNRKVNQGTGALLSPTDQALSRAEVAHPLL 589 Query: 594 TLYQVVGNKDKG-------WQGKDFWLPNIKLP 619  LY++ G  D         W     W+PNIKLP Sbjct: 590 ILYRIEGVNDAAAQRGEPTWSSDPIWVPNIKLP 622

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 126

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 251> which encodes amino acid sequence <SEQ ID 252; NGS128>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.98   Possible cleavage site: 20 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 7.37 threshold:  0.0   PERIPHERAL Likelihood = 7.37    modified ALOM score: −1.97 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.225(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_11357195 gi|11387l95|sp|Q50976|T2F7_NEIGO TYPE II RESTRICTION ENZYME NGOFVII (ENDONUCLEASE NGOFVII) (R.NGOFVII) (R.NGOVII) pir||T10166 restriction endonuclease (EC 3.1.21.-) NgoVII-N. gonorrhoeae gb|AAA86271.1|(U43736) R.NgoVII [Neisseria gonorrhoeae] Length = 326 Score = 651 bits (1679), Expect = 0.0 Identities = 317/326 (97%), Positives = 320/326 (97%) Query: 1 MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI 60 MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI Sbjct: 1 MNTVFSNIANAKITEKSLNAVWMDLFKSADEVLMATGYVSNDAVVELHKILELNDHIQKI 60 Query: 61 DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI 120 DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI Sbjct: 61 DLLVGMHYLEGFSHLQYDSLCKLNDFLRHEKRGAVYVSPFVKFHGKMYSFKNYQKINGLI 120 Query: 121 GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH 180 GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH Sbjct: 121 GSANLTCFWDSTERTYETMLHLNGKPAQILQADIQSTIHKLGKNIQEVERPSKFIEHNSH 180 Query: 181 LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY 240 LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY Sbjct: 181 LENCLGVQKIAPEQIRQLFAQTSEYHFSIPAKTEEKSNLNVFFGEGRRDKRGFVKPRPWY 240 Query: 241 EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKNFRSENDLKTLGKWIKGR 300 EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSK    + +LKTLGKWIKGR Sbjct: 241 EVELIVSKDITSQEGYPVLKSFTVITDDGWQFQCKTSGDYSKTSTQKMNLKTLGKWIKGR 300 Query: 301 LESHGCLQNNEKITHETLREYGNDHF 326 LESHGCLQNNEKITHETLREYGN+ F Sbjct: 301 LESHGCLQNNEKITHETLREYGNESF 326

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 127

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 253> which encodes amino acid sequence <SEQ ID 254; NGS 129>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −5.5   Possible cleavage site: 48 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 10.03 threshold:  0.0   PERIPHERAL Likelihood = 10.03    modified ALOM score: −2.51 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----     bacterial cytoplasm --- Certainty= 0.545(Affirmative) < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>    bacterial outer membrane --- Certainty= 0.000(Not Clear) < succ>    bacterial inner membrane --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15804186 gi|15804186|ref|NP_290225.1|\(NC_002655) DNA-damage- inducible protein [Escherichia coli O157:H7 EDL933] ref|NP_312547.1|(NC_002695) DNA-damage-inducible protein [Escherichia coli O157:H7] gb|AAG58789.1|AE005591_13 (AE005591) DNA-damage-inducible protein [Escherichia coli O157:H7 EDL933] dbj|BAB37943.1|(AP002566) DNA-damage-inducible protein [Escherichia coli O157:H7] Length = 278 Score = 340 bits (872), Expect = 2e−92 Identities = 161/266 (60%), Positives = 197/266 (73%) Query: 1 MTTENNAFENAKHIDETGNEYWSARTLQQILEYSEWRNFQRAIDKAITACETSGNDKNHH 60 M   +  FE  +H    G E+WSAR L  +L+Y +WRNFQ+ + +A  ACE S    + H Sbjct: 5 MNEHQPFEEIRHYGTEGQEFWSARELAPLLDYRDWRNFQKVLAPATQACEASNQAASDH 64 Query: 61 FVETNKMIALGKGGQREVADYRLSRYACYLIVQNGDPSKSVIAAGQTYFAVQARRQELQD 120 FVET KM+LG G QRE+ D  LSRYACYL+VQNGDP+K VIAAGQTYFA+Q RRQEL D Sbjct: 65 FVETTKMVVLGSGAQRELEDVHLSRYACYLVVQNGDPAKPVIAAGQTYFAIQTRRQELAD 124 Query: 121 EAAFRSLGEDKQRLLLRRQLREHNTDLAAAAKDAGVEKPVEYAVFQNHGYRGLYGGLDKQ 180 + AF+ L ED++RL LR +L+EHN  L  AA+ A V    ++A+FQNHGY+GLYGGLD++ Sbjct: 125 DEAFKQLREDEKRLFLRNELKEHNKQLVEAAQQAAVATATDFAIFQNHGYQGLYGGLDQK 184 Query: 181 GIHSPRGLKKSQRILDHMNASEPAANLFRATQTEEKLRRKNIQGKTQANRVHFEVGQKVR 240  IH  KGLKKSQ+ILDHM ++E AANLFRATQTEEKL+R  +  K QAN  HF+VG KVR Sbjct: 185 AIEQLKGLKKSQKILDHMGSTELAANLFRATQTEEKLKRDGVNSKQQANTTHFDVGSKVR 244 Query: 241 QTIEELGGIMPENQPVPEKSIKQLEN 266 QTI+ELGG MPE  P P+ SIKQLEN Sbjct: 245 QTIQELGGTMPEELPTPQVSIKQLEN 270

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 128

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 255> which encodes amino acid sequence <SEQ ID 256; NGS130>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −3.68   Possible cleavage site: 14 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 3 value: −3.45 threshold:  0.0   INTEGRAL Likelihood = −3.45 Transmembrane 68-84 (68-92)   INTEGRAL Likelihood = −1.59 Transmembrane 10-26 (10-26)   INTEGRAL Likelihood = −1.44 Transmembrane 46-62 (45-62)   PERIPHERAL Likelihood =   1.48    modified ALOM score: 1.19 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.238(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_17988861 gi|17998861|ref|NP_541494.1|\(NC_003318) hypothetical protein [Brucella melitensis] gb|AAL53758.1|(AE009687) hypothetical protein [Brucella melitensis] Length = 99 Score = 108 bits (270), Expect = 3e−23 Identities = 59/91 (64%), Positives = 69/91 (74%) Query: 11 LLFSCMLAVTCPTRLIGFFALRNRTLSRRAQTVMEAAPGCVLISVIAPYFVSDKPHELIA 70 L    M +VT  TR+ G+  LRNRTLS RA  VMEAAPGCVLISVIAP FVSDKP  LIA Sbjct: 8 LTILAMASVTYLTRIGGYVLLRNRTLSNRAMAVMEAAPGCVLISVIAPDFVSDKPANLIA 67 Query: 71 IALTAFAACRFSMLFTVLIGVGSSGISGWLM 101 +A+T FAA RFSML TVLIG+G++ I  +L+ Sbjct: 6 LAVTVFAATRFSMLPTVLIGMGAASICRYLI 98

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 129

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 257> which encodes amino acid sequence <SEQ ID 258; NGS131>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −1.65   Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 7.05 threshold:  0.0   PERIPHERAL Likelihood = 7.05    modified ALOM score: −1.91 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.152(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_16760390 gi|16760390|ref NP_456007.1|\(NC_003198) hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi] emb|CAD01841.1|(AL621270) hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi] Length = 227 Score = 104 bits (259), Expect = 2e−21 Identities = 68/221 (30%), Positivies = 115/221 (51%), Gaps = 11/221 (4%) Query 2 DKEKVLDKIKKCLALGRSVNEHEAAQALRQAQALMEKYKVNAEDIALSKVSEQKAD--RK 59 D++K ++K+KK LAL  S N HEAA ALR+A+ LM+ + +   DIA+S + E  + Sbjct: 3 DQDKHIEKLKKLLALAASGNPHEAALALRRARKLMDVHGITHSDIAMSDIDETISHYWPT 62 Query: 60 MAFKLAGWQWGVANMIADIFGCKSYQRGKT---MMFYGIGNRAETSAYAFDVVYRQISAD 116  + +   +  G+ N+I + FG  S     T   + FYG   RA  +AY ++V+ RQ+ Sbjct: 63 GSLRPPRYMLGLMNIIREAFGVNSIIHPGTYPGVGFYGNRERAALAAYTWEVLARQLKKA 122 Query: 117 RRKFLKT-CRAGKPSHRTYLADPFCGGWIASAWETVKKFEMSDEEKAIMDGYKKKEYPDM 175 R++++    +  K + RT   D+F  GW+ +    ++ F ++D+E+ +M  + + +YP Sbjct: 123 RQQYISAQNKRIKTATRTSRGDQFAEGWVLAVISEIQSFALTDDERELMQQWLEHKYPQT 182 Query: 176 AEARTRDAKSSILQGSKMEYEALTRGMESGKQVKLHYAVNG 216    R R    S   G    Y     G   G+ V+LH  V+G Sbjct: 183 QTTRARKPGRS-RNGDASRY----AGFREGQNVRLHRPVSG 218

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 130

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 259> which encodes amino acid sequence <SEQ ID 260; NGS132>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.06   Possible cleavage site: 30 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 2.49 threshold:  0.0   PERIPHERAL Likelihood = 2.49    modified ALOM score: −1.00 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.075(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 131

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 261> which encodes amino acid sequence <SEQ ID 262; NGS133>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 1.64   Possible cleavage site: 53 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 3.82 threshold:  0.0   PERIPHERAL Likelihood = 3.82    modified ALOM score: −1.26 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.068(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to the following sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 132

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 263> which encodes amino acid sequence <SEQ ID 264; NGS135>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.67   Possible cleavage site: 39 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 5.52 threshold:  0.0   PERIPHERAL Likelihood = 5.52    modified ALOM score: −1.60 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.457(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 133

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 265> which encodes amino acid sequence <SEQ ID 266; NGS136>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −3.97   Possible cleavage site: 15 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 11.35 threshold:  0.0   PERIPHERAL Likelihood = 11.35    modified ALOM score: −2.77 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.523(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to sequences in the databases:

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 134

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 267> which encodes amino acid sequence <SEQ ID 268; NGS 137>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −8.52   Possible cleavage site: 51 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 2.81 threshold:  0.0   PERIPHERAL Likelihood = 2.81    modified ALOM score: −1.06 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.374(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 135

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 269> which encodes amino acid sequence <SEQ ID 270; NGS138>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −7   Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 10.66 threshold:  0.0   PERIPHERAL Likelihood = 10.66    modified ALOM score: −2.63 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.415(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_13559865 gi|13559865|ref|NP_112075.1|\(NC_002730) terminase small subunit [Bacteriophage HK620] gb|AAK28890.1|AF335538_42 (AF335538) terminase small subunit [Bacteriophage HK620] Length = 140 Score = 125 bits (313), Expect = 5e−28 Identities = 56/122 (45%), Positivies = 85/122 (68%) Query: 4 TKRKLGRPTDYTKDMADKICEKIANGRSLRSICAEDGVPPMKTIYRWLEANEEFRHQYAR 63 T+ K GRP+DY  ++AD IC  +++G SL  +C   G+P   T++RWL  +E+FR +YA+ Sbjct: 3 TEPKAGRPSDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHEDFRDKYAK 62 Query: 64 AREKQADYFAEEIIEIADSAQAESAAVSKAKLQIDARKWAASKIAPKKYGDKSELDVKSGDG 125 A E +AD   EEI EIAD+A  ++A V+KA+L++D RKWA +++ P+KYGDK   ++   DG Sbjct: 63 ATEARADSIFEEIFEIADNAIPDAAEVAKARLRVDTRKWALARMNPRKYGDKVTNELVGKDG 124

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 136

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 271> which encodes amino acid sequence <SEQ ID 272; NGS139>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −1.49   Possible cleavage site: 32 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 8.65 threshold:  0.0   PERIPHERAL Likelihood = 8.65    modified ALOM score: −2.23 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.301(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_16127009 gi|16127009|ref|NP_421573.1|\(NC_002696) hypothetical protein [Caulobacter crescentus] gb|AAK24741.1|(AE005943) hypothetical protein [Caulobacter crescentus] Length = 184 Score = 59.7 bits (143), Expect = 4e−08 Identities = 50/164 (30%), Positives = 74/164 (44%), Gaps = 20/164 (12%) Query: 30 ASGREFRTAYYTYPQWRFSLSFEVLRTKASVNELEKLAGFFNARKGSFESFLYEDPAD-- 87 ASG E RT+ ++  + R+ ++         ++E+ +L  FF AR+G    F + DPAD Sbjct: 5 ASGHERRTSPWSQSRRRYLIA----TAPRPLDEIAELVAFFEARRGRLHGFRFRDPADFK 60 Query: 88 -------NAVTDQPVGNTVQGAR-YQLVRSMGGFIEPVSAVKERP-----AVKVGGTAL 134         A  DQ +G T  GV + +QL ++ G   E V+    +P      V V G  L Sbjct: 61 SCAPSVQPAAGDQAIG-TGDGVRKKAFQLRKTYGAGGEAVARTIAKPVAGTVTVAVAGVVL 119 Query: 135 AYGRDYTVTDKGVLVFNTPQPPGRPITWTGGFYFRVRFTSDTVD 178 A G        G++  NT  P G  +T    F   VRF  D +D Sbjct: 120 APGAFAVDVTTGLITLNTAPPAGAAVTAGFAFDTPVRFDLDRLD 163

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 137

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 273> which encodes amino acid sequence <SEQ ID 274; NGS140>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −3.86   Possible cleavage site: 31 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1 value: −4.94 threshold:  0.0   INTEGRAL Likelihood = −4.94 Transmembrane 34-50 (31-54)   PERIPHERAL Likelihood = 8.01    modified ALOM score: 1.49 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.297(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_17987625 gi|17987625|ref|NP_540259.1|\(NC_003317) Hypothetical Phage Protein [Brucella melitensis] gb|AAL52523.1|(AE009572) Hypothetical Phage Protein [Brucella melitensis] Length = 144 Score = 72.4 bits (176), Expect = 5e−12 Identities = 43/119 (36%), Positives = 64/119 (53%), Gaps = 7/119 (5%) Query: 10 RIVEEARSWLGTPYHHHAMVKGAGVDCAMLLVAVYGAV-GLLPEGFDPRPYPQDWHLHRD 68 R++ EA  W+GTPY H A   G   DC  L+  ++A+ G+ PE  +P  Y  DW Sbjct: 6 RVLAEAHRWIGTPYRHGASTLGVSCDCLGVRQIWRALYGVEPE--NPGVYAPDWAEVSQ 63 Query: 69 CERYLGFVTQFC--RETESPQAGDIAV--WRFGRSFSHGGILAGGGKVIHSYIGRGVVS 123  +  L    ++   RE  +PQ GD+  W+ G +  H GI+A  G+ IH+Y G GV++ Sbjct: 64 GDPMLEAAVRYMVRREEHAPQPGDLLVFRWKPGFAAKHMGIMAREGRFIHAYQGHGVLA 122

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 138

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 275> which encodes amino acid sequence <SEQ ID 276; NGS141>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 5.35   Possible cleavage site: 28 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 29 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 8.86 threshold:  0.0   PERIPHERAL Likelihood = 8.86    modified ALOM score: −2.27 Score for OM-PP discrimination: 1.53 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: 1.53 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Outer membrane? Score: 0.152929 Outer membrane? Score: 0.152929 ----- Final Results -----     bacterial outer membrane --- Certainty= 0.512(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.320(Affirmative) < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear)       < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_5915870 gi|5915870|sp|Q50940|CAH_NEIGO Carbonic anhydrase precursor (Carbonate dehydratase) emb|CAA72038.1|(Y11152) carbonic anhydrase [Neisseria gonorrhoeae] Length = 252 Scare = 523 bits (1347), Expect = e−147 Identities = 252/252 (100%), Positives = 252/252 (100%) Query: 1 MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ 60 MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ Sbjct: 1 MPRFPRTLPRLTAVLLLACTAFSAAAHGNHTHWGYTGHDSPESWGNLSEEFRLCSTGKNQ 60 Query: 61 SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGTYTLKQFHFH 120 SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGTYTLKQFHFH Sbjct: 61 SPVNITETVSGKLPAIKVNYKPSMVDVENNGHTIQVNYPEGGNTLTVNGTYTLKQFHFH 120 Query: 121 VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN 180 VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN Sbjct: 121 VPSENQIKGRTFPMEAHFVHLDENKQPLVLAVLYEAGKTNGRLSSIWNVMPMTAGKVKLN 180 Query: 181 QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR 240 QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR Sbjct: 181 QPFDASTLLPKRLKYYRFAGSLTTPPCTEGVSWLVLKTYDHIDQAQAEKFTRAVGSENNR 240 Query: 241 PVQPLNARVVIE 252 PVQPLNARVVIE Sbjct: 241 PVQPLNARVVIE 252

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 139

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 277> which encodes amino acid sequence <SEQ ID 278; NGS142>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −0.49   Possible cleavage site: 22 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 1.22 threshold:  0.0   PERIPHERAL Likelihood = 1.22    modified ALOM score: −0.74 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----       bacterial cytoplasm --- Certainty= 0.145(Affirmative)       < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15794480 gi|15794480|ref|NP_284302.1|\(NC_003116) hypothetical protein [Neisseria meningitidis Z2491] pir||F81851 hypothetical protein NMA1587 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB84814.1|(AL162756) hypothetical protein [Neisseria meningitidis Z2491] Length = 181 Score = 358 bits (919), Expect = 6e−98 Identities = 173/181 (95%), Positives = 178/181 (97%) Query: 1 LKTDTARMNNLIPEHLAAYAHSDNLQIEGGHRCFSLSCQGRDTFHIRYYGEPFDGLITDT 60 +KTDTA+MNNLIPEHLAAYAHSD+LQIEG HRCFSLSCQGRDTFHIRYYGEPFDGL+TDT Sbjct: 1 MKTDTAKMNNLIPEHLAAYAHSDSLQIEGVHRCFSLSCQGRDTFHIRYYGEPFDGLMTDT 60 Query: 61 DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYSQNQKQNRTLTDLDEYTYRVPIHL 120 DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYS NQKQNRTLTDLDEYTYRV IHL Sbjct: 61 DKAPVKIVAVEAVSGDEIVLFDGAEHGYNAMFCDKYSPNQKQNRTLTDLDEYTYRVLIHL 120 Query: 121 YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAISIDLIDEKHSVRELLNEELS 181 YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAIS+DLIDEKHSVRELLNEELS Sbjct: 121 YYNIDYEDEYEDFVNSEGQVPLIDGRIISFDSLKRNGFDAISVDLIDEKHSVRELLNEELS 181

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS142 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 140

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 279> which encodes amino acid sequence <SEQ ID 280; NGS143>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −2.51   Possible cleavage site: 57 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 4 value: −15.23 threshold:  0.0   INTEGRAL Likelihood = −15.23 Transmembrane  84-100 (79-107)   INTEGRAL Likelihood = −8.12 Transmembrane 259-275 (250-281)   INTEGRAL Likelihood = −4.14 Transmembrane 159-175 (153-176)   INTEGRAL Likelihood = −3.88 Transmembrane 216-232 (216-235)   PERIPHERAL Likelihood =   1.11    modified ALOM score: 3.55 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.709(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_5764059 gi|5764059|emb|CAB53350.1|\(AJ010260) NosR protein [Paracoccus denitrificans] Length = 724 Score = 393 bits (1009), Expect = e−108 Identities = 191/379 (50%), Positives = 249/379 (65%), Gaps = 22/379 (5%) Query: 1 LMVQRVLSVNDKAFVTADLDYELPQAYYVDDPKAPPVEISAPVEAVPAAASDTASDGIAE 60 L+VQR +   +K F T DL Y+LPQ Y      AP         A PAA +D Sbjct: 358 LLVQREVGPIEKVFHTFDLGYQLPQKYLRSIAPAPEA---------AAPAAQAD-------- 402 Query: 61 DASAENGVSNQLWKQIWAKQGQIVVVGIALTILLLVFLFQDWIVRYEKWYDRFRFAFLT 120     E+   QLWK+IW   + +I  +   L +L  VF FQ +  RYE+ +  FR A+LT Sbjct: 403 ----ESQAQAQLWKRIWLDSKPKIAGLAAMLLVLTGVFFFQSFTTRYERAFYVFRMAYLT 458 Query: 121 FTLFYIGWYAQAQLSVVNTLTLFSAILTEFHWEFFLMDPIVFILWLFTAATMLLWNRGTF 180  TL ++GWYA AQLSVVN + LF +++  F W+ FL+DP+ FILW   AA +L W RG + Sbjct: 459 VTLVFLGWYANAQLSVVNLMALFGSLVNGFSWQAFLLDPLTFILWFAVAAALLFWGRGAY 518 Query: 181 CGWLCPFGSLQELTNRIAKKLGVKQITVPHMLHTRLNVIKYLILFGFLAISLYDLGTAEK 240 CGWLCPFG+LQELTN++A+KL + Q T+P  LH RL  +KY+I  G   +SL  +  AE Sbjct: 519 CGWLCPFGALQELTNQVARKLRIPQWTLPWGLHERLWPVKYMIFLGLFGVSLMSVEQAEH 578 Query: 241 FAEVEPFKTAIILKFMCDWWFVAPAVALLIAGLFIERFFCRYLCPLGAGIALPGRFRVFD 300  AEVEPFKTAIILKF+  W FVA+A ALLIAGLF+ERF+CRYLCPLGA +A+P R R+FD Sbjct: 579 LAEVEPFKTAIILKFIRAWPFVAYAAALLIAGLFVERFYCRYLCPLGAALAIPARMRMFD 638 Query: 301 WLRRYKMCGNPCQICTHBCPVQAIAPEGDIHPNECIQCLHCQVMYHHDTRCPQVVAENKK 360 WL+RY  CGNPCQ C  +CPVQ+I P G+I+PNECI CLHCQV+Y  +T CP V+   KK Sbjct: 639 WLKRYHECGNPCQTCARQCPVQSIHPTGEINPNECINCLHCQVLYQSETTCPVVI---KK 695 Query: 361 KQKQAAAKSGELENVSKQP 379  +++ A  +G +  + + P Sbjct: 696 LKRREAVAAGSMPKLGQPP 714

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 141

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 281> which encodes amino acid sequence <SEQ ID 282; NGS144>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 1.23   Possible cleavage site: 21 >>> May be a lipoprotein Amino Acid Composition of Predicted Mature Form:   calculated from 20 ALOM: Finding transmembrane regions (Klein et al.)   count: 1 value: −0.37 threshold:  0.0   INTEGRAL Likelihood = −0.37 Transmembrane 90-106 (89-106)   PERIPHERAL Likelihood = 10.82    modified ALOM score: 0.57 Rule: inner or outer membrane protein Rule: inner or outer membrane protein Rule: cytoplasmic membrane protein *** Reasoning Step: 2 Lipoprotein? Inner membrane? ----- Final Results -----     bacterial outer membrane --- Certainty= 0.790(Affirmative)     < succ>     bacterial inner membrane --- Certainty= 0.734(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology no to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 142

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 283> which encodes amino acid sequence <SEQ ID 284; NGS145>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 1.5   Possible cleavage site: 19 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 20 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 8.70 threshold:  0.0   PERIPHERAL Likelihood = 8.70    modified ALOM score: −2.24 Score for OM-PP discrimination: −9.24 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −9.24 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 0.924443 Periplasmic space? Score: 0.924443 ----- Final Results -----   bacterial periplasmic space --- Certainty= 0.931(Affirmative) < succ>     bacterial outer membrane --- Certainty= 0.231(Affirmative)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear)       < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_5051426 gi|5051426|emb|CAB45007.1|\(AJ242839) OpcA protein [Neisseria gonorrhoeae] Length = 263 Score = 531 bits (1369), Expect = e−150 Identities = 262/263 (99%), Positives = 263/263 (99%) Query: 1 MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA 60 MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA Sbjct: 1 MKKALLALTIAAISGTAMAQLPDFLGKGEYTVRTDISKQTLKNADLKEKHKVQKNIGFRA 60 Query: 61 DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDVEEKRTDVYAGYTYTQPISEAT 120 DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDV+EKRTDVYAGYTYTQPISEAT Sbjct: 61 DMPFDDIHHGMRFEVSHSRDKKDMYVVTESTTKPFGKDVKEKRTDVYAGYTYTQPISEAT 120 Query: 121 KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD 180 KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD Sbjct: 121 KLRAGLGLGYEKYKDAVANEKGTVSTEREAFYTKAHADLTSDLGGGWYLNPWAEVKVDLD 180 Query: 181 AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL 240 AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL Sbjct: 181 AKLKHNATVAGVSADINAKTRGWGVGVGANIGKQITDTVGIEAGPFYKHRHFKASGSFVL 240 Query: 241 DGGNIRVDPTKINEYGVRVGVKF 263 DGGNIRVDPTKINEYGVRVGVKF Sbjct: 241 DGGNIRVDPTKINEYGVRVGVKF 263

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 143

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 285> which encodes amino acid sequence <SEQ ID 286; NGS146>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 0.1   Possible cleavage site: 51 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 52 ALOM: Finding transmembrane regions (Klein et al.)   count: 0 value: 3.50 threshold:  0.0   PERIPHERAL Likelihood = 3.50    modified ALOM score: −1.20 Score for OM-PP discrimination: −15.70 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −15.70 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 1.56979 Periplasmic space? Score: 1.56979 ----- Final Results -----   bacterial periplasmic space --- Certainty= 0.944(Affirmative) < succ>     bacterial outer membrane --- Certainty= 0.375(Affirmative)     < succ>     bacterial inner membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear)       < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_5051429 gi|5051429|emb|CAB45013.1|\(AJ242839) hypothetical protein [Neisseria gonorrhoeae] Length = 109 Score = 216 bits (549), Expect = 2e−55 Identities = 109/109 (100%), Positives = 109/109 (100%) Query: 1 MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYVLKITALTLLWSAASFLLWQKKPQPA 60 MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYVLKITALTLLWSAASFLLWQKKPQPA Sbjct: 1 MFKRPEEIIVLILAVLWIAGTYFLAALFGADAYVLKITALTLLWSAASFLLWQKKPQPA 60 Query: 61 YLAAAARLPDHLLVAVASESIGRTRFFTLACIMDVQHNLSPDSRNRRLSV 109 YLAAAARLPDHLLVAVASESIGRTRFFTLACIMDVQHNLSPDSRNRRLSV Sbjct: 61 YLAAAARLPDHLLVAVASESIGRTRFFTLACIMDVQHNLSPDSRNRRLSV 109

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 144

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 287> which encodes amino acid sequence <SEQ ID 288; NGS147>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): −4.09   Possible cleavage site: 40 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)   count: 1 value: −2.28 threshold:  0.0   INTEGRAL Likelihood = −2.28 Transmembrane 36-52 (36-52)   PERIPHERAL Likelihood = 5.20    modified ALOM score: 0.96 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.191(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_6606516 gi|6606516|gb|AAF19189.1|AF200716_2 \(AF200716) trafficking protein B [Neisseria gonorrhoeae] Length = 139 Score = 274 bits (700), Expect = 7e−73 Identities = 139/139 (100%), Positivies = 139/139 (100%) Query: 2 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH 61 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH Sbjct: 1 MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLH 60 Query: 62 ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT 121 ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT Sbjct: 61 ERLEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSLTVAT 120 Query: 122 RDTGSFFAADVAVFNPWHD 140 RDTGSFFAADVAVFNPWHD Sbjct: 121 RDTGSFFAADVAVFNPWHD 139

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 145

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 289> which encodes amino acid sequence <SEQ ID 290; NGS148>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)   Signal Score (−7.5): 0.86   Possible cleavage site: 47 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 48 ALOM: Finding transmembrane regions (Klein et al.)   count: 5 value: −15.44 threshold:  0.0   INTEGRAL Likelihood = −15.44 Transmembrane 157-173 (142-181)   INTEGRAL Likelihood = −12.15 Transmembrane  62-78 (56-83)   INTEGRAL Likelihood = −6.32 Transmembrane 194-210 (191-212)   INTEGRAL Likelihood = −4.30 Transmembrane  87-103 (85-104)   INTEGRAL Likelihood = −2.60 Transmembrane 121-137 (121-142)   PERIPHERAL Likelihood = 2.92    modified ALOM score: 3.59 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty= 0.718(Affirmative)     < succ>   bacterial periplasmic space --- Certainty= 0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty= 0.000(Not Clear)     < succ>       bacterial cytoplasm --- Certainty= 0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15777859|gi|15777859|gb|AAL05955.1|\(AY048756) putative cadmium binding protein [Staphylococcus aureus] Length = 209 Score = 354 bits (908), Expect = 1e−96 Identities = 177/208 (85%), Positives = 194/208 (93%) Query: 14 MRCFMFSTVITAAVLYIATAVDLLVILLIFFARANTRKEYRDIYIGQYLGSVILILVSLF 73 MRC M  TV+TAAVLYIATAVDLLVILLIFFARA TRKEYRDIY+GQYLGS+ILILVSLF Sbjct: 1 MRCIMIQTVVAAAVLYIATAVDLLVILLIFFARAKTRKEYRDIYVGQYLGSIILILVSLF 60 Query: 74 LAFVLNYVPEKWVLGLLGLIPIYLGIKVAIYDDCEGEKRAKKELDEKGLSKLVGIVALVT 133 LAFVLNYVPEKW+LGLLGLIPIYLGIKVAIYDDCEGEKRAKKEL+EKGLSKLVG VA+VT Sbjct: 61 LAFVLNYVPEKWILGLLGLIPIYLGIKVAIYDDCEGEKRAKKELNEKGLSKLVGTVAIVT 120 Query: 134 VASCGADNIGLFVPYFVTLDLVDLLVTLLVFLILIFVLVYTAQRLANISGVGEIVEKFSR 193 +ASCGADNIGLFVPYFVTL + +LL+TL VFLILIF LV+TAQ+LANI G+GEIVEKFSR Sbjct: 121 IASCGADNIGLFVPYFVTLSVTNLLLTLFVFLILIFFLVFTAQKLANIPGIGEIVEKFSR 180 Query: 194 WIMAVIYIGLGLFIIIENNTIRTIISII 221 WIMA+IYI LGLFIIIEN+TI+TI+  I Sbjct: 181 WIMAIIYIALGLFIIIENDTIQTILGFI 208

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 146

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 291> which encodes amino acid sequence <SEQ ID 292; NGS149>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.63    Possible cleavage site: 43 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 2.12 threshold: 0.0    PERIPHERAL Likelihood = 2.12    modified ALOM score: −0.92 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.122(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15675455 gi|15675455|ref|NP_269629.1|\(NC_002737) conserved hypothetical protein [Streptococcus pyogenes] [Streptococcus pyogenes M1 GAS] gb|AAK34350.1|(AE006588) conserved hypothetical protein [Streptococcus pyogenes M1 GAS] Length = 224 Score = 106 bits (264), Expect = 3e−22 Identities = 63/151 (41%), Positives = 85/151 (55%), Gaps = 12/151 (7%) Query: 20 LSALQHYAFCPRQCALIHNEQAWAENYLTAQGKALHERVDSDE-PETCKGVRFEWTVHVL 78 LS +QH+ FC RQ ALIH EQ W +N  TA G+ LH + D+    E  K +     + + Sbjct: 11 LSGIQHFQFCKRQWALIHIEQQWLDNEATAHGQVLHTKADNPYIKEKRKELLVSRAMPIS 70 Query: 79 ADKLGISGILDLVE---------VDTKTGRLKP--VEYKRGKPKPDPGDEIQLCAQGLCL 127 + +LG+SGI+D+VE         +  K G+  P  VEYKRGKPK D  D +QL AQ +CL Sbjct: 71 SAELGLSGIMDVVEFYKDDQGVSLRGKRGKWLPKVVEYKRGKPKKDTRDIVQLVAQTMCL 130 Query: 128 EEMTGQTVSEGALWYMQTRHRVPVVFSDGLR 158 EE     ++EG L+Y     RV V  +  LR Sbjct: 131 EETLDCDINEGCLYYHSVNQRVIVPMTSALR 161

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 147

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 293> which encodes amino acid sequence <SEQ ID 294; NGS150>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.71    Possible cleavage site: 19 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −0.85 threshold: 0.0    INTEGRAL Likelihood = −0.85 Transmembrane    79-95 (79-96)    PERIPHERAL Likelihood = 6.52    modified ALOM score: 0.67 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.134(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>        bacterial cytoplasm --- Certainty=        0.000(Not Clear) < succ>

The protein has no homology to sequences in the databases.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 148

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 295> which encodes amino acid sequence <SEQ ID 296; NGS151>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): 3.47    Possible cleavage site: 23 >>> Seems to have a cleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 24 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 14.32 threshold: 0.0    PERIPHERAL Likelihood = 14.32    modified ALOM score: −3.36 Score for OM-PP discrimination: −32.29 Rule: outer membrane or periplasmic protein Score for OM-PP discrimination: −32.29 Rule: outer membrane or periplasmic protein *** Reasoning Step: 2 Periplasmic space? Score: 3.22889 Periplasmic space? Score: 3.22889 ----- Final Results -----     bacterial periplasmic space --- Certainty=     0.933(Affirmative) < succ>     bacterial outer membrane --- Certainty=     0.253(Affirmative) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>        bacterial cytoplasm --- Certainty=        0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gsa_AAY75310 Neisseria gonorrheae ORF 649 protein sequence SEQ ID N0:2094|WO9957280-A2|21-MAR-2000 Length = 103 Score = 35.4 bits (80), Expect = 0.32 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 5/85 (5%) Query: 7 ILTGILLATALPASAHGMHKSKPLAMDELPPIQQYFKRAETCYNKAGNKADFARN-NTK 65 + T     T+ PA  H  H SK      L P C++Y +R    Y   GN  +   N   + Sbjct: 13 VSTTAAAGTSEPAHRHTKHISKA-NKQMLHPECRKYLERRAAWYRSQGNVQELRENKKAR 71 Query: 66 FLFQALPAADLGQRKQMCQIAMDSF 90   F+ LP A   ++K  C+ A ++F Sbjct: 72 KAFRTLPYA---EQKIQCRAAYEAF 93

The protein was expressed in E.coli as a soluble 9.35 kDa His-fusion product and then purified.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 149

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 297> which encodes amino acid sequence <SEQ ID 298; NGS152>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.46    Possible cleavage site: 18 >>> Seems to have an uncleavable N-term signal seq Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −3.19 threshold: 0.0    INTEGRAL Likelihood = −3.19 Transmembrane    368-384 (367-384)    PERIPHERAL Likelihood = 0.53    modified ALOM score: 1.14 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.227(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>        bacterial cytoplasm --- Certainty=        0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gsa_AAY81609 Streptococcus pneumoniae type 4 protein sequence #109 |WO200006737-A2|24-MAY-2000 Length = 1237 Score = 48.1 bits (113), Expect = 4e−04 Identities = 80/312 (25%), Positives = 142/312 (44%), Gaps = 59/312 (18%) Query: 57 RRQARIRVGNLITDSLEHIRVKALLPLPL----KLPVKRI---NLPRNLPALPVRLRKTI 109 RRQ R +   ++   L+H RV  L   P+    ++PV+++    +PR   A   RL++ + Sbjct: 941 RRQVR-QPQQVLVHQLQHQRVHRLRRQPVHQSQQVPVRQLPHQQVPRLQQAPVRRLQQVL 999 Query: 110 SPRQIGDALPILKLQRI--RLTLHLKPLPLHPQLGLLHIKRPVRIPLRHLAVQRTLVRLN 167 +P+      P+ + Q++  RL  H +  PL   L      +P R  +  L  QR  VRLN Sbjct: 1000 APQP--QPQPVRQPQQVSQRLNRHQRVRPLQQVLA----PQPQRQQVHRL--QRQRVRLN 1051 Query: 168 RRIKPPLLQHRLTVRRILRRSRRQPFPAQFPDRRIFIMFRHNPARRIKLCRRQLTVQGPR 227 R  +   LQ  L               A  P R+     +H   +R++  ++ L  Q  R Sbjct: 1052 RHQRVRPLQQVL---------------APQPQRQQVHRLQH---QRVRPLQQVLAPQPQR 1093 Query: 228 IRRSRPLIKLPLLRRQRIRPGRHQRTLRVKITHRLAAPIHIPVKSQRRRRPSARIRRARI 287  +  R       L+RQR+R  +HQR  + +  H+L   +H PV+ Q + R + ++++  + Sbjct: 1094 QQVHR-------LQRQRVRLSQHQRVRQPQQAHQL-LNLHQPVR-QPQHRQAPQLQQVPV 1144 Query: 288 APREIRPGPRIGGKRLIAARKP-QTGIRTPFESTRPAQPPRPILNIVTAQIHHIPITRR 345    + R   R+   + +  R+P Q  +R P    R  + P+P+ LN       H P+ R+ Sbjct: 1145 RQPQRRQVRRL---QQVPVRQPQQVPVRQP--QRRQVRRPQPVHLN------ RHQPV-RQ 1192 Query: 346 PGLIIRNGTPHR 357 P  ++ +   H+ Sbjct: 1193 PQQVLVHQLQHQ 1204

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 150

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 299> which encodes amino acid sequence <SEQ ID 300; NGS153>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.48    Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.31 threshold: 0.0    PERIPHERAL Likelihood = 6.31    modified ALOM score: −1.76 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.150(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15832758 gi|15832758|ref|NP_311531.1|\(NC_002695) hypothetical protein [Escherichia coli O157:H7] dbj|BAB36927.1|(AP002562) hypothetical protein [Escherichia coli O157:H7] Length = 188 Score = 73.9 bits (180), Expect = 3e−12 Identities = 54/169 (31%), Positives = 79/169 (45%), Gaps = 15/169 (8%) Query: 12 LTQEVLKELLRYDDNTGKLYWAERPRKYFNSGLHYKSWNTGFSGKEVFLYKGRLGYLKLK 71 LT + + ELL +D +TG   W    +      +   S    F            GY  + Sbjct: 16 LTVKRIFELLSFDKSTGVFRWKVPTQ----GRIALNSVAGAFDSN------------GYSMIM 62 Query: 72 IFKKQYNAHRLIWLFVYGKH-ASSIGHINRDKTDNRISNLRDVTHAENMKNRGKFKNNTS 130 I  ++Y  H L++   + +  A  I H+N  +TDNR  NLR+    EN +N    KN+ S Sbjct: 63 IDGRRYKTHVLVFYITHNRWPAGQIDHNGIRTDNRPENLRECLPIENSRNIRIRKNSKS 122 Query: 131 GHTGVYFKPSKKWQARIWINRKNKILGLFEHIEDAA-KAREAASKDFG 178 G  GV +HK  KKW  R+  + K+K  G F+ +E A   A EA  K +G Sbjct: 123 GCRGVTWMKRQKKWNVRLGFHGKSKHFGCFDDLELAVLVAEEARDKYYG 171

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 151

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 301> which encodes amino acid sequence <SEQ ID 302; NGS154>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.98    Possible cleavage site: 28 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 8.12 threshold: 0.0    PERIPHERAL Likelihood = 8.12    modified ALOM score: −2.12 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.423(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15830449 gi|15830449|ref|NP_309222.1|\(NC_002695) hypothetical protein [Escherichia coli O157:H7] dbj|BAA94132.1|(AP000422) hypothetical protein [Escherichia coli O157:H7] dbj|BAB346l8.1|(AP002554) hypothetical protein [Escherichia coli O157:H7] Length = 148 Score = 42.7 bits (99), Expect = 0.003 Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 10/99 (10%) Query: 37 IRPRKSKRSVEQNRRLWFLYREISEKVFIDGRRFSQDVWHE-----FLKRKFIGCIEHPN 91 +  ++ KRS  QN R+W +  ++S +V   G+R + + W +     +LK K +    +P Sbjct: 33 VHVKEPKRSKAQNDRMWPMLNDVSRQVLWHGQRLAPEDWKDLFTALWLKTKKLEQRSVPG 92 Query: 92 GQ----LMGISTTKLSVEEMSEYQEKIISWASNEHGVLW 126       ++G+ T+K+    M+E  E I+ W   E  V W Sbjct: 93 IDGGVVMLGVRTSKMRKASMTELIE-IMFEFGSERNVRW 130

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 152

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 303> which encodes amino acid sequence <SEQ ID 304; NGS155>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −4    Possible cleavage site: 27 >>> Seems to have an uncleavable N-term signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.98 threshold: 0.0    PERIPHERAL Likelihood = 4.98    modified ALOM score: −1.50 *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.046(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>        bacterial cytoplasm --- Certainty=        0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_15801502 gi|15801502|ref|NP_287519.1|\(NC_002655) putative endonuclease of prophage CP-9330 [Escherichia coli O157:H7 EDL933] ref|NP_309804.1|(NC_002695) endonuclease [Escherichia coli O157:H7] gb|AAG56131.1|AE005344_7 (AE005344) putative endonuclease of prophage CP-933O [Escherichia coli O157:H7 EDL933] dbj|BAB35200.1|(AP002556) endonuclease [Escherichia coli O157:H7] Length = 119 Score = 47.4 bits (1111, Expect = 2e−04 Identities = 38/122 (31%), Positives = 54/122 (44%), Gaps = 8/122 (6%) Query: 71 LILPYPVSANRYWRIWRNRAVRSAEAAAYKETVRRIA-QGAGAMPSEGAVAVYVRLIPKA 129 L+LPYP + N YWR   +    S     Y+  V  I  Q    +   G +A+ +   P Sbjct: 5 LVLPYPPTVNTYWERRGSTYFVSKAGERYRRAVVLIVRQQRLKLSLSGRLAIKIIABP-- 62 Query: 130 NKDGGANKTVIDLDNLKVTLDALQGVAYHNDRQVRRIAAEYGGEPVTGGGLAVEVGELE 189       +K   DLDN LK  LDAL       D +           G+PV+GG L V++ ++E Sbjct: 63 -----PDKRRRDLDNILKAPLDALTHAGVLMDDEQFDEINIVRGQPVSGGRLGVKIYKIE 117 Query: 190 ME 191  E Sbjct: 118 SE 119

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 153

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 305> which encodes amino acid sequence <SEQ ID 306; NGS156>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −2.61    Possible cleavage site: 49 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.96 threshold: 0.0    PERIPHERAL Likelihood = 7.96    modified ALOM score: −2.09 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.307(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gsa_AAG90098 C glutamicum protein fragment SEQ ID NO: 3852 |EP1108790-A2|26-SEP-2001 Length = 148 Score = 102 bits (253), Expect = 7e-21 Identities = 60/147 (40%). Positives = 88/147 (59%), Gaps = 18/147 (12%) Query: 3 NAYDVADFFLSPFEEEDGEQISNLKLQKLLYYAQGYALAILNRPLFAENIEHWQHGPVVP 62 +A ++A++F++  +E D E +S LKLQKLLYY+QG  +A   R LF++ I  WQHGPV P Sbjct: 5 SAREIAEWFVAWGDELDAE-VSPLKLQKLLYYSQGEHIAATGRKLFSDKILAWQHGPVTP 63 Query: 63 CIYRTYKKYGGSPLPAAHIEPDKYADEEL---------VVLNRVRKEQGCYTAWALRNKT 113  +Y   K YG +P     I+PD++  E            L  V ++ G Y+AWALR KT Sbjct: 64 GVYSDTKSYGRNP-----IDPDEFVSDEFNWDDYSDVSDELVTVWRKYGIYSAWALREKT 118 Query: 114 HQEAPWIQT-RQGEVIGI--AIMGEYF 137 H E+PW+    QG+ I I  A + ++F Sbjct: 119 HSESPWLDAWAQGQNIEITDAALKDFF 145

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 154

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 307> which encodes amino acid sequence <SEQ ID 308; NGS157>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.65    Possible cleavage site: 42 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 3.98 threshold: 0.0    PERIPHERAL Likelihood = 3.98    modified ALOM score: −1.30 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.291(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: {circumflex over ( )} **gbp_6274533 gi|6274533|gb|AAF06681.1|AF163663_6 \(AF058689) Toul [Neisseria meningitidis] Length = 272 Score = 546 bits (1408), Expect e−154 Identities = 267/272 (98%), Positives = 271/272 (99%) Query: 19 MKGMDKLRYQRDFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDVYSPAK 78 MKGMDKLRYQ+DFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDVYS AK Sbjct: 1 MKGMDKLRYQQDFLNIRPIFTAGEQEYLTELSDRLPLSVLTDSVRNIEEIGIDVYSSAK 60 Query: 79 LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSPKPFDWLDFLKT 138 LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSP+PFDWLDFLKT Sbjct: 61 LEGNTYNQYDTQALLKLGQTAGGKLYSDAVMLINLRESYRHLLSGLDSPEPFDWLDFLKT 120 Query: 139 THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA 198 THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA Sbjct: 121 THSLISENLLEKGSGGVVRRDSVTISGTDYTPLSNPQSLDTELKWLLQEAPKIENPFDRA 180 Query: 199 VYLHNNLAYLRYFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY 258 VYLHNNLAYL+YFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY Sbjct: 181 VYLHNNLAYLQYFKDCNKRTARNCMTLSLMRSGFFPCVFSPDSYPAYAEAVVAYYETGDY 240 Query: 259 GLFKKYFISAYENTVNKYGPQPDVDIFRNFSI 290 GLFKKYFISAYENTVNKYGPQPDVDIFRNFS+ Sbjct: 241 GLFKKYFISAYENTVNKYGPQPDVDIFRNFSL 272

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS157 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 155

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 309> which encodes amino acid sequence <SEQ ID 310; NGS158>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −6.98    Possible cleavage site: 18 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 0.16 threshold: 0.0    PERIPHERAL Likelihood = 0.16    modified ALOM score: −0.53 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.185(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: > {circumflex over ( )}{circumflex over ( )} **gbp_15791833 gi|15791833|ref|NP_281656.1|\(NC_002163) amino-acid ABC transporter ATP-binding protein [Campylobacter jejuni] pir||H81391 amino-acid ABC transporter ATP-binding protein Cj0469 [imported]-Campylobacter jejuni (strain NCTC 11168) emb|CAB75107.1|(AL139075) amino-acid ABC transporter ATP-binding protein [Campylobacter jejuni] Length = 253 Score = 301 bits (772), Expect = 6e−81 Identities = 153/244 (62%), Positives = 195/244 (79%), Gaps = 2/244 (0%) Query: 1 MALLSIRKLHKQYGSVAIQSLDLDLEKGEVIVLLGPSGCGKSTLLRCVNGLEPHQGGSI 60 M++L I  L K YGS  A++ ++L+++  EV+V+LGPSGCGKSTLLRC+NGLE G+I Sbjct: 1 MSILKIENLQKYYGSHHALKDINLEVKAKEVVVILGPSGCGKSTLLRCINGLEEIASGNI 60 Query: 61 VMDGVGEFGKDVS-WQTARQKVGMVFQSYELFAHMTVIENILLGPVKVQNRDRAEAEAQA 119  +D   +  KD   W RQKVGMVFQSYELF H++V ENILLGP+KVQ R + E   +A Sbjct: 61 YIDNE-KIDKDFKEWPRMRQKVGMVFQSYELFEHLSVEENILLGPMKVQKRKKDEVLKEA 119 Query: 120 GKLLERVGLLDRKNAYPRELSGGQKQRIAIVRALCLNPEVILLDEITAALDPEMVREVLE 179    LE+VGLL + +AYPRELSGGQKQRIAIVR+LC+NPE++L DE+TAALDPE+VREVLE Sbjct: 120 KIWLEKVGLLHKIHAYPRELSGGQKQRIAIVRSLCMNPELMLFDEVTAALDPEIVREVLE 179 Query: 180 VVLELAREGMSMLIVTHEMGFARKVADRIVFMDKGGIVESSDPETFFSAPKSERARQFLA 239 V+L LA+EGM+MLIVTHEMGFA+ VAD+I+FMD+G I+E +DP++FF  PKSERA++FL Sbjct: 180 VMLNLAKEGMTMLIVTHEMGFAKAVADKIIFMDEGKIIEENDPKSFFKNPKSERAKKFLN 239 Query: 240 GMDY 243   DY Sbjct: 240 LFDY 243

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 156

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 311> which encodes amino acid sequence <SEQ ID 312; NGS159>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −4.16    Possible cleavage site: 13 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 6.47 threshold: 0.0    PERIPHERAL Likelihood = 6.47    modified ALOM score: −1.79 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.312(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: > {circumflex over ( )}{circumflex over ( )} **gbp_15794799 gi|1579479.9|ref|NP_284621.1|\(NC_003116) hypothetical protein [Neisseria meningitidis Z2491] pir||B81819 hypothetical protein NMA1914 [imported]- Neisseria meningitidis (group A strain Z2491) emb|CAB85135.1|(AL162757) hypothetical protein [Neisseria meningitidis Z2491] Length = 206 Score = 265 bits (678), Expect = 8e−70 Identities = 131/146 (89%), Positives = 138/146 (93%) Query: 1 MTKLYAQIAKTEAQDDGTVKVWGYASSEAVDSDGEVVAAEAMKAAIPDYMKFGAVREMHG 60 MTKLYA+IAK E QDDGTVKVWGYASSE +DSDGEV+AA AMKAAIPDYMKFGA REMHG Sbjct: 1 MTKLYAEIAKMETQDDGTVKVWGYASSEEIDSDGEIAAAAMKAAIPDYMKFGAGREMHG 60 Query: 61 SNAAGTAIEINVEDDGRTFFGAHIVDPVAVTKVKTGVYKGFSIGGSVTARNDLNKSQITG 120 SNAAGTAIEINVEDDG TFFGAHI+DPV V+KVKTGVYKGFSIGGSVTAR+DLNKSQITG Sbjct: 61 SNAAGTAIEINVEDDGITFFGAHIIDPVVVSKVKTGVYKGFSIGGSVTARDDLNKSQITG 120 Query: 121 LKLTEISLVDRPANPDAVFTCFKADK 146 LKLTEISL+DRPANPDAV TCFKADK Sbjct: 121 LKLTEISLIDRPANPDAVSTCFKADK 146

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS159 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 157

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 313> which encodes amino acid sequence <SEQ ID 314; NGS160>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −8.3    Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 7.85 threshold: 0.0    PERIPHERAL Likelihood = 7.85    modified ALOM score: −2.07 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.407(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: > {circumflex over ( )}{circumflex over ( )} **gbp_2126352 gi|2126352|pir||JC5218 type I site-specific deoxyribonuclease (EC 3.1.21.3) Hsd chain S [validated]-Pasteurella haemolytica gb|AAC44667.1|(U46781) HSDS [Mannheimia haemolytica] Length = 442 Score = 97.1 bits (240), Expect = 3e−19 Identities = 55/149 (36%), Positives = 81/149 (53%), Gaps = 3/149 (2%) Query: 26 EVAEYSKNRICSDKLNEHNYVGVDNLLQNREGKKLSGYVPSEGKMTEYIVNDILIGNIRP 85 ++E    +I    L + NY+  DN+L N  G  L+  +P+      +   DIL  NIR Sbjct: 10 DIVELISEKIKIKDLKKENYISTDNMLPNFGGITLAENLPNSASCNRFAKKDILFSNIRT 69 Query: 86 YLKKIWQADCTGGTNGDVLVIRV--TDEKVNPKYLYQVLADDKFFAFNMKHAKGAKMPRG 143 Y KK+W A+ +GG + DVLV+R   TD  +N +YL+ ++  D F  F +  A GAKMPRG Sbjct: 70 YFKKVWLAEFSGGCSPDVLVMRSKNTDILLN-EYLFLLIRSDDFINFTVISANGAKMPRG 128 Query: 144 SKAAIMQYKIPIPPLPEQEKIVAILGKFD 172  K A+  +   IP +  Q+K +A    FD Sbjct: 129 DKNAMKGFIFNIPSIEYQKKCIANYFAFD 157

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 158

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 315> which encodes amino acid sequence <SEQ ID 316; NGS161>. Analysis of this protein sequence reveals the following: GvH Examining signal sequence (von Heijne)    Signal Score (−7.5): −5.08    Possible cleavage site: 36 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 1 value: −1.59 threshold: 0.0    INTEGRAL Likelihood = −1.59 Transmembrane    302-318 (302-318)    PERIPHERAL Likelihood = 3.76    modified ALOM score: 0.82 Rule: cytoplasmic membrane protein *** Reasoning Step: 2 ----- Final Results -----     bacterial inner membrane --- Certainty=     0.164(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>        bacterial cytoplasm --- Certainty=        0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: pir||E81921 probable DNA-invertase NMA0772 [imported]-Neisseria meningitidis (group A strain Z2491) emb|CAB84055.1|(AL162754) putative DNA-invertase [Neisseria meningitidis Z2491] Length = 321 Score = 295 bits (755), Expect = 9e−79 Identities = 151/322 (46%), Positives = 216/322 (66%), Gaps = 3/322 (0%) Query: 14 LRNAVGLDISKLTFDATAIVGNAEYSKFDNDSKGLDQFSDRLKSLGCQNLHICMEATGN 73 +RNAVGLDIS  TFD   I+       KF ND +G     + + +   +++++CMEATGN Sbjct: 1 MRNAVGLDISAKTFDVVTIINGETDYRKFSNDEQGCKNLKEWISAKREKDIYVCMEATGN 60 Query: 74 YYEEVADYFAQYYSVYVVNPLKISKYAESRFKRTKTDKQDAKLIAQYCRSAQESELVKRQ 133 YYE+ AD  A+ Y V V+NPLKI  YA+ RF R K DKQDAKLIA++C++A   EL KR+ Sbjct: 61 YYEQAADCLAEEYHVSVINPLKIKAYAQKRFSRVKNDKQDAKLIAEFCQTALIEELPKRE 120 Query: 134 KPTDEQYRLSRMTAAYAQIKSECAAMKNRHHAAKDEEAAKAYAEIIKAMNEQLEVLKEKI 193 KPT++QY L R+ +  +Q+  +  + KNR  AAKD    K + + +K +   L  +K+KI Sbjct: 121 KPTEQQYSLKRLLSLQSQLLEQQTSQKNRIRAAKDSFVQKIHEKQLKELENHLNAVKKKI 180 Query: 194 KEQTEKPN--CKEGVKRLETIPAIGRMTAAVLFHHLTSSKFETSNKFAAFAGLSPQQKES 251  +QT K +   KE KRLETIP++G+ TA  L  +L +S FE + +FA +AGL+P Q  S Sbjct: 181 -DQTIKSDKKMKELTKRLETIPSVGKTTAISLMSYLINSTFENAKQFTAYAGLNPHQNIS 239 Query: 252 GTSVRGKGKLTKFGNRKLRAVLFMPAMVAYRIRAFPDFIKRLEEKKKPKKVIIAALMRKL 311 GTSV  K K+TK+GNR++R  LFM A+VA++   FP F  RL++ KKPK +II ALMRK+ Sbjct: 240 GTSVNKKSKMTKYGNRRIRGSLFMAALVAFKNNYFPAFTNRLKKAKKPKMLIIGALMRKI 299 Query: 312 AVIAYHVHKKGGDYDPSRYKSA 333  V+A++++K   D+D +RY++A Sbjct: 300 LVVAFNLYKTETDFDKTRYQTA 321

A homolog was found in serogroup A N.meningitidis but not in serogroup B, so NGS161 protein and nucleic acid are useful for distinguishing between gonococcus and serogroup B N.meningitidis.

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 159

A DNA sequence was identified in N.gonorrhoeae <SEQ ID 983> which encodes amino acid sequence <SEQ ID 984; NGS162>. Analysis of this protein sequence reveals the following: GvH: Examining signal sequence (von Heijne)    Signal Score (−7.5): −0.86    Possible cleavage site: 33 >>> Seems to have no N-terminal signal seq. Amino Acid Composition of Predicted Mature Form:   calculated from 1 ALOM: Finding transmembrane regions (Klein et al.)    count: 0 value: 4.08 threshold: 0.0    PERIPHERAL Likelihood = 4.08    modified ALOM score: −1.32 Rule: cytoplasmic protein *** Reasoning Step: 2 ----- Final Results -----        bacterial cytoplasm --- Certainty=        0.032(Affirmative) < succ>     bacterial periplasmic space --- Certainty=     0.000(Not Clear) < succ>     bacterial outer membrane --- Certainty=     0.000(Not Clear) < succ>     bacterial inner membrane --- Certainty=     0.000(Not Clear) < succ>

The protein has homology to the following sequences in the databases: ref|NP_312507.1|(NC_002695) hypothetical protein [Escherichia coli O157:H7] gb|AAG5B749.1|AE005587_7 (AE005587) putative adhesin [Escherichia coli O157:H7 EDL933] dbj|BAB37903.1|(AP002566) hypothetical protein [Escherichia coli O157:H7] Length = 1588 Score = 120 bits (302), Expect = 4e−26 Identities = 109/359 (30%), Positives = 170/359 (46%), Gaps = 65/359 (18%) Query: 22 AVALGSSSTASGEYSYASGYNSVASGNKSYAAGYASVASAEGSVVIGDSRQVKPEADQGV 81 + A+G  + A G+YS A G  + A G  S A G ++++  + S+ +G S     +    + Sbjct: 93 STAVGYDAIAEGQYSSAIGSKTHAIGGASMAFGVSAISEGDRSIALGASSYSLGQYSMAL 152 Query: 82 AVGSKATVKNKAKQRVVVGSEAKVNAERGIAIGKEAKAGGKTTNTLLDGPAYYADAIAVG 141    SKA      K  + +G  +K      IA+G   KA    T  +         +IA+G Sbjct: 153 GRYSKAL----GKLSIAMGDSSKAEGANAIALGNATKA----TEIM---------SIALG 195 Query: 142 YQAEAGKGGAIALGKQAKATKQNGMALGVESEAAGDFSTAVGNESKAKGQGG-------- 193   A A K  ++ALG  + A+++N +A+G E+EAA + +TA+GN +KAKG Sbjct: 196 DTANASKAYSMALGASSVASEENAIAIGAETEAA-ENATAIGNNAKAKGTNSMAMGFGSL 254 Query: 194 ------VGLGNQSKAEADFAVAV--GNKAEATKE------------NSLVIGRYARANGN 233       + LGN S+A AD A+A+  GNKA+                N++ +G  + A G+ Sbjct: 255 ADKVNTIALGNGSQALADNAIAIGQGNKADGVDAIALGNGSQSRGLNTIALGTASNATGD 314 Query: 234 HSVSLGSRSEIKDGVSNSVAPGYGSVASENNVVSVAYKETPQSTELSYRKIVGVDDGV-- 291  S++LGS S   +G+ NSVA G  S+A  +N VSV             RKIV V +G Sbjct: 315 KSLALGSNSS-ANGI-NSVALGADSIADLDNTVSVGNSSLK-------RKIVNVKNGAIK 365 Query: 292 -NDFDAVNVRQLKAMQGQNMAELFSVRSEVRGVAASSAALSALTPLSYDANNPTQFMVG 349  + +DA+N  QL A+         SV   + G AA       +T  +Y+  N ++ VG Sbjct: 366 SDSYDAINGSQLYAISD-------SVAKRLGGGAAVDVDDGTVTAPTYNLKNGSKNNVG 417 Score = 86.3 bits (212), Expect = 1e−15 Identities = 68/253 (26%), Positives = 118/253 (45%), Gaps = 39/253 (15%) Query: 28 SSTASGEYSYASGYNSVASGNKSYAAGYASVASAEGSVVIGDSRQVKPEADQGVAVGSKA 87 S+  +G    + G  + A  +      Y S ++ +G V IG               G+KA Sbjct: 38 SALVAGGMLSSFGALANAGNDNGQGVDYGSGSAGDGWVAIGK--------------GAKA 83 Query: 88 -TVKNKAKQRVVVGSEAKVNAERGIAIGKEAKAGGKTTNTLLDGPAYYADAIAVGYQAEA 146  T  N +     VG +A    +   AIG +  A G  +             +A G  A + Sbjct: 84 NTFMNTSGSSTAVGYDAIAEGQYSSAIGSKTHAIGGAS-------------MAFGVSAIS 130 Query: 147 GKGGAIALGKQAKATKQNGMALGVESEAAGDFSTAVGNESKAKGQGGVGLGNQSKAEADF 206     +IALG  + +  Q  MALG  S+A G  S A+G+ SKA+G   + LGN +KA Sbjct: 131 EGDRSIALGASSYSLGQYSMALGRYSKALGKLSIAMGDSSKAEGANAIALGNATKATEIM 190 Query: 207 AVAVGNKAEATKENSLVIGRYARANGNHSVSLGSRSEIKDGV-----------SNSVAPG 255 ++A+G+ A A+K  S+ +G  + A+  +++++G+ +E  +             +NS+A G Sbjct: 191 SIALGDTANASKAYSMALGASSVASEENAIAIGAETEAAENATAIGNNAKAKGTNSMAMG 250 Query: 256 YGSVASENNVVSV 268 +GS+A + N +++ Sbjct: 251 FGSLADKVNTIAL 263

Based on this analysis, it was predicted that this protein from N.gonorrhoeae, and its epitopes, could be useful antigens for vaccines or diagnostics.

EXAMPLE 160

Further open reading frames were identified in gonococcus <SEQ IDs 317/318 to 8621/8622>. These polypeptide and nucleotide sequences are useful for studying gonococcus, for diagnostic purposes, as antibiotic targets, and as vaccine antigens.

It will be understood that the invention has been described by way of example only and modifications may be made whilst remaining within the scope and spirit of the invention. 

1. A protein comprising an amino acid sequence selected from the group consisting of SEQ IDs 26, 72, 230, 984, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 30, 32, 34, 36, 38, 40, 42, 44,46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, 206, 208, 210, 212, 214, 216, 218, 220, 222, 224, 226, 228, 232, 234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314 and 316:
 2. A protein having 50% or greater sequence identity to a protein according to claim
 1. 3. A protein comprising a fragment of an amino acid sequence selected from the group consisting of 26, 72, 230, 984, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204,206,208, 210, 212,214, 216, 218,220,222, 224, 226, 228, 232,234, 236, 238, 240, 242, 244, 246, 248, 250, 252, 254, 256, 258, 260, 262, 264, 266, 268, 270, 272, 274, 276, 278, 280, 282, 284, 286, 288, 290, 292, 294, 296, 298, 300, 302, 304, 306, 308, 310, 312, 314 and
 316. 4. An antibody which specifically binds to a protein according to any one of claims 1 to
 3. 5. A nucleic acid molecule which encodes a protein according to any one of claims 1 to
 3. 6. A nucleic acid molecule according to claim 5, comprising a nucleotide sequence selected from the group consisting of SEQ IDs 25, 71, 229, 983, 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313 and
 315. 7. A nucleic acid molecule comprising a fragment of a nucleotide sequence selected from the group consisting of SEQ IDs 25, 71, 229, 983, 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313 and
 315. 8. A nucleic acid molecule comprising a nucleotide sequence complementary to a nucleic acid molecule according to any one of claims 5 to
 7. 9. A nucleic acid molecule comprising a nucleotide sequences having 50% or greater sequence identity to a nucleic acid molecule according to any one of claims 5 to
 8. 10. A nucleic acid molecule which can hybridise to a nucleic acid molecule according to any one of claims 5 to 9 under high stringency conditions.
 11. A composition comprising a protein, a nucleic acid molecule, or an antibody according to any preceding claim.
 12. A composition according to claim 11 being a vaccine composition or a diagnostic composition.
 13. A composition according to claim 11 or claim 12 for use as a pharmaceutical.
 14. The use of a composition according to claim 13 in the manufacture of a medicament for the treatment or prevention of infection due to streptococcus bacteria, particularly N.gonorrhoeae.
 15. A process for distinguishing N.gonorrhoeae from N.meningitidis, comprising the steps of: (a) contacting a protein, a nucleic acid molecule, or an antibody according to any one of claims 1 to 10 with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes. 